Pathway Analysis for FABIA (1 ~ 10 Biclusters, thresL criterion)
John Zhuang
2024-08-08
library(multiMiR)## Welcome to multiMiR.
##
## multiMiR database URL has been set to the
## default value: http://multimir.org/
##
## Database Version: 2.3.0 Updated: 2020-04-15library(clusterProfiler)## ## clusterProfiler v4.12.2 Learn more at https://yulab-smu.top/contribution-knowledge-mining/
##
## Please cite:
##
## S Xu, E Hu, Y Cai, Z Xie, X Luo, L Zhan, W Tang, Q Wang, B Liu, R Wang,
## W Xie, T Wu, L Xie, G Yu. Using clusterProfiler to characterize
## multiomics data. Nature Protocols. 2024, doi:10.1038/s41596-024-01020-z##
## Attaching package: 'clusterProfiler'## The following object is masked from 'package:multiMiR':
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## select## The following object is masked from 'package:stats':
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## filterlibrary(org.Hs.eg.db)## Loading required package: AnnotationDbi## Loading required package: stats4## Loading required package: BiocGenerics##
## Attaching package: 'BiocGenerics'## The following objects are masked from 'package:stats':
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## IQR, mad, sd, var, xtabs## The following objects are masked from 'package:base':
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## anyDuplicated, aperm, append, as.data.frame, basename, cbind,
## colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find,
## get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply,
## match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
## Position, rank, rbind, Reduce, rownames, sapply, setdiff, table,
## tapply, union, unique, unsplit, which.max, which.min## Loading required package: Biobase## Welcome to Bioconductor
##
## Vignettes contain introductory material; view with
## 'browseVignettes()'. To cite Bioconductor, see
## 'citation("Biobase")', and for packages 'citation("pkgname")'.## Loading required package: IRanges## Loading required package: S4Vectors##
## Attaching package: 'S4Vectors'## The following object is masked from 'package:clusterProfiler':
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## rename## The following object is masked from 'package:utils':
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## findMatches## The following objects are masked from 'package:base':
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## expand.grid, I, unname##
## Attaching package: 'IRanges'## The following object is masked from 'package:clusterProfiler':
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## slice## The following object is masked from 'package:grDevices':
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## windows##
## Attaching package: 'AnnotationDbi'## The following object is masked from 'package:clusterProfiler':
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## select## library(stringr)
library(ggplot2)0. Loading of Results
A. List of all Gene names in the dataset
gene.names = readRDS("data/derived/unique_gene_names.rds")B. Selected Features
Due to long computational time to obtain gene names for microRNA and to execute pathway analysis,
pathway analysis will only be done for 1, 2, 3, 5 and 10-bicluster FABIA.
results.fabia = readRDS("data/sel_features/results_fabia_extracted_by_bic.rds")
sel.features = results.fabia[1:5]
sel.features## $`1bc`
## $`1bc`$bicluster1
## G6PD.RPPA TGM2.R2Gn hsa-mir-1185-1 hsa-mir-1185-2 hsa-mir-1197
## -0.5664688 -0.5495991 0.7662391 0.6351004 0.6196432
## hsa-mir-127 hsa-mir-134 hsa-mir-136 hsa-mir-154 hsa-mir-299
## 0.5556598 0.5553999 0.5555263 0.5772620 0.5401860
## hsa-mir-323 hsa-mir-323b hsa-mir-329-1 hsa-mir-329-2 hsa-mir-337
## 0.5936458 0.6038210 0.6858061 0.6838698 0.4938656
## hsa-mir-369 hsa-mir-370 hsa-mir-376a-1 hsa-mir-376a-2 hsa-mir-376b
## 0.5261986 0.5848124 0.5874765 0.6262681 0.5265671
## hsa-mir-376c hsa-mir-377 hsa-mir-379 hsa-mir-380 hsa-mir-381
## 0.5575709 0.6136535 0.5312722 0.6782381 0.5273689
## hsa-mir-382 hsa-mir-409 hsa-mir-410 hsa-mir-411 hsa-mir-412
## 0.5608688 0.5577673 0.5278594 0.6712205 0.4479444
## hsa-mir-431 hsa-mir-432 hsa-mir-433 hsa-mir-485 hsa-mir-487a
## 0.5105189 0.5210694 0.6026199 0.6385659 0.7267015
## hsa-mir-487b hsa-mir-493 hsa-mir-494 hsa-mir-495 hsa-mir-496
## 0.5397963 0.4263443 0.6434824 0.5006743 0.5717559
## hsa-mir-517a hsa-mir-539 hsa-mir-541 hsa-mir-543 hsa-mir-654
## -0.5002749 0.5285802 0.6543345 0.6088287 0.5726739
## hsa-mir-655 hsa-mir-656 hsa-mir-665 hsa-mir-668 hsa-mir-758
## 0.6905221 0.8365020 0.5754425 0.6625089 0.5231312
## hsa-mir-770 hsa-mir-889
## 0.6163359 0.5576494
##
##
## $`2bc`
## $`2bc`$bicluster2
## G6PD.RPPA RBM15.RPPA FASN.RPPA TTF1.RPPA VHL.RPPA
## -0.4947514 0.3795670 0.5768981 -0.4377838 -0.3772156
## TGM2.R2Gn SQSTM1.R2Gn hsa-mir-1185-1 hsa-mir-1185-2 hsa-mir-1193
## -0.5100910 -0.4078596 0.5594705 0.4696187 0.3940719
## hsa-mir-1197 hsa-mir-1258 hsa-mir-127 hsa-mir-134 hsa-mir-136
## 0.4989459 -0.3781580 0.4464493 0.4475944 0.4489271
## hsa-mir-154 hsa-mir-299 hsa-mir-323 hsa-mir-323b hsa-mir-329-1
## 0.4516122 0.4297408 0.4716776 0.4642313 0.5510674
## hsa-mir-329-2 hsa-mir-337 hsa-mir-369 hsa-mir-370 hsa-mir-376a-1
## 0.6231958 0.4337406 0.4375161 0.4669418 0.4945849
## hsa-mir-376a-2 hsa-mir-376b hsa-mir-376c hsa-mir-377 hsa-mir-379
## 0.4993865 0.4425174 0.4439293 0.4885167 0.4269243
## hsa-mir-380 hsa-mir-381 hsa-mir-382 hsa-mir-409 hsa-mir-410
## 0.5553450 0.4251795 0.4438641 0.4433247 0.4366585
## hsa-mir-411 hsa-mir-412 hsa-mir-431 hsa-mir-432 hsa-mir-433
## 0.4690795 0.4240978 0.4598986 0.4625162 0.4727682
## hsa-mir-466 hsa-mir-485 hsa-mir-487a hsa-mir-487b hsa-mir-493
## -0.4874996 0.4465527 0.5465899 0.4492726 0.4061574
## hsa-mir-494 hsa-mir-495 hsa-mir-496 hsa-mir-506 hsa-mir-507
## 0.4714333 0.3996444 0.4620112 -0.5175712 -0.5847532
## hsa-mir-508 hsa-mir-509-1 hsa-mir-509-2 hsa-mir-509-3 hsa-mir-510
## -0.5014800 -0.4582238 -0.4606885 -0.4641817 -0.7000950
## hsa-mir-513a-1 hsa-mir-513a-2 hsa-mir-513b hsa-mir-513c hsa-mir-514-1
## -0.5146970 -0.5416414 -0.4808000 -0.4772028 -0.5008222
## hsa-mir-514-2 hsa-mir-514-3 hsa-mir-514b hsa-mir-517a hsa-mir-539
## -0.5045772 -0.5027646 -0.4337189 -0.3707787 0.4324968
## hsa-mir-541 hsa-mir-543 hsa-mir-605 hsa-mir-654 hsa-mir-655
## 0.5403953 0.4310786 -0.4237129 0.4606440 0.5126972
## hsa-mir-656 hsa-mir-665 hsa-mir-668 hsa-mir-758 hsa-mir-770
## 0.6667496 0.5263446 0.5101166 0.4220787 0.5519820
## hsa-mir-889
## 0.4446168
##
## $`2bc`$bicluster1
## FN1.R2Gn CTNNB1.R2Gn CCND1.R2Gn hsa-mir-1185-1 hsa-mir-1185-2
## -0.4511588 -0.4925327 -0.4626447 0.5297352 0.4314716
## hsa-mir-135b hsa-mir-206 hsa-mir-3166 hsa-mir-3199-1 hsa-mir-323b
## -0.3906779 -0.4583481 -0.4034852 0.4173045 0.3852651
## hsa-mir-329-1 hsa-mir-376a-2 hsa-mir-380 hsa-mir-3923 hsa-mir-411
## 0.4048227 0.3728961 0.3843573 -0.3936415 0.4946514
## hsa-mir-433 hsa-mir-485 hsa-mir-487a hsa-mir-494 hsa-mir-506
## 0.3724767 0.4700524 0.4803354 0.4429761 0.4240878
## hsa-mir-507 hsa-mir-508 hsa-mir-509-1 hsa-mir-509-2 hsa-mir-509-3
## 0.5126687 0.4074888 0.4327297 0.4354988 0.4239098
## hsa-mir-510 hsa-mir-513a-1 hsa-mir-513a-2 hsa-mir-514-1 hsa-mir-514-2
## 0.5448665 0.3938817 0.4365787 0.4445967 0.4491853
## hsa-mir-514-3 hsa-mir-514b hsa-mir-543 hsa-mir-655 hsa-mir-656
## 0.4515958 0.4196900 0.4407581 0.4666229 0.4984523
## hsa-mir-668
## 0.4212441
##
##
## $`3bc`
## $`3bc`$bicluster2
## G6PD.RPPA FASN.RPPA TGM2.R2Gn hsa-mir-1185-1 hsa-mir-1197
## -0.6514624 0.8737953 -0.7011726 0.7013345 0.6522884
## hsa-mir-329-1 hsa-mir-329-2 hsa-mir-376a-2 hsa-mir-380 hsa-mir-466
## 0.7064830 0.8107564 0.6617729 0.7212568 -0.6553467
## hsa-mir-487a hsa-mir-506 hsa-mir-507 hsa-mir-508 hsa-mir-509-3
## 0.7015375 -0.7206063 -0.8075650 -0.6905181 -0.6404349
## hsa-mir-510 hsa-mir-513a-1 hsa-mir-513a-2 hsa-mir-513b hsa-mir-513c
## -0.9915946 -0.7202971 -0.7574027 -0.6739789 -0.6583085
## hsa-mir-514-1 hsa-mir-514-2 hsa-mir-514-3 hsa-mir-541 hsa-mir-605
## -0.7000274 -0.7049369 -0.7023947 0.7012658 -0.6444571
## hsa-mir-655 hsa-mir-656 hsa-mir-665 hsa-mir-668 hsa-mir-770
## 0.6524373 0.8623823 0.6826397 0.6457786 0.7249692
##
## $`3bc`$bicluster3
## GATA3.RPPA IGFBP2.R2Gn FN1.R2Gn CTNNB1.R2Gn CCND1.R2Gn
## -0.9248231 -0.6582546 -0.8641139 -0.9724582 -0.9043804
## hsa-mir-1185-1 hsa-mir-124-3 hsa-mir-135b hsa-mir-206 hsa-mir-2114
## 0.6907430 -0.7375579 -0.6885645 -0.8045228 0.9326673
## hsa-mir-3166 hsa-mir-3199-1 hsa-mir-3655 hsa-mir-3923 hsa-mir-3926-2
## -0.7932514 0.8070724 0.7332915 -0.7798807 0.7178644
## hsa-mir-411 hsa-mir-485 hsa-mir-487a hsa-mir-506 hsa-mir-507
## 0.6875457 0.6667901 0.6462570 1.0799827 1.3110639
## hsa-mir-508 hsa-mir-509-1 hsa-mir-509-2 hsa-mir-509-3 hsa-mir-510
## 1.0634858 1.1021953 1.1088305 1.0805202 1.3487461
## hsa-mir-513a-1 hsa-mir-513a-2 hsa-mir-513b hsa-mir-513c hsa-mir-514-1
## 1.0030912 1.1041617 0.9312010 0.9159748 1.1088941
## hsa-mir-514-2 hsa-mir-514-3 hsa-mir-514b hsa-mir-582
## 1.1209338 1.1254595 1.0572493 -0.6426409
##
## $`3bc`$bicluster1
## G6PD.RPPA ERBB3.R2Gn FN1.R2Gn CDH2.R2Gn CTNNB1.R2Gn
## -0.7822392 0.6635589 -0.8509824 -0.6757206 -0.9033705
## TGM2.R2Gn CCND1.R2Gn hsa-mir-1185-1 hsa-mir-1185-2 hsa-mir-1197
## -0.6468656 -0.8457685 1.3503645 1.1107468 0.9529190
## hsa-mir-1269 hsa-mir-127 hsa-mir-1270-2 hsa-mir-134 hsa-mir-135b
## -0.8010780 0.8771463 0.6597144 0.8552275 -0.7632553
## hsa-mir-136 hsa-mir-154 hsa-mir-206 hsa-mir-299 hsa-mir-3144
## 0.8799115 0.9404601 -0.9422025 0.8557165 -0.6628892
## hsa-mir-3166 hsa-mir-3199-1 hsa-mir-323 hsa-mir-323b hsa-mir-329-1
## -0.7309786 0.7773116 0.9517043 1.0090382 1.0896878
## hsa-mir-329-2 hsa-mir-337 hsa-mir-3655 hsa-mir-369 hsa-mir-370
## 0.9268612 0.7072687 0.6453038 0.7971572 0.9256967
## hsa-mir-376a-1 hsa-mir-376a-2 hsa-mir-376b hsa-mir-376c hsa-mir-377
## 0.8889023 0.9533043 0.7822999 0.8807044 0.9724277
## hsa-mir-379 hsa-mir-380 hsa-mir-381 hsa-mir-382 hsa-mir-3923
## 0.8279896 1.0380931 0.8185154 0.9003822 -0.6993006
## hsa-mir-409 hsa-mir-410 hsa-mir-411 hsa-mir-431 hsa-mir-432
## 0.8873264 0.8137013 1.2199026 0.7062762 0.7375277
## hsa-mir-433 hsa-mir-485 hsa-mir-487a hsa-mir-487b hsa-mir-494
## 1.0121041 1.1513445 1.2182208 0.8302603 1.0982661
## hsa-mir-495 hsa-mir-496 hsa-mir-510 hsa-mir-517a hsa-mir-520a
## 0.7997866 0.9103087 0.6889123 -0.9189714 -0.6468570
## hsa-mir-539 hsa-mir-541 hsa-mir-543 hsa-mir-577 hsa-mir-654
## 0.8272746 0.9954855 1.0942886 -0.6592411 0.9080437
## hsa-mir-655 hsa-mir-656 hsa-mir-665 hsa-mir-668 hsa-mir-758
## 1.1825263 1.3173936 0.7805161 1.1096351 0.8120464
## hsa-mir-770 hsa-mir-889
## 0.8385361 0.8914403
##
##
## $`5bc`
## $`5bc`$bicluster2
## G6PD.RPPA FASN.RPPA INPP4B.RPPA TTF1.RPPA PRDX1.RPPA
## -1.2236772 1.2175965 -0.9125127 -0.8930760 -0.8458281
## G6PD.R2Gn TGM2.R2Gn SQSTM1.R2Gn hsa-mir-1185-1 hsa-mir-1185-2
## -0.7505276 -1.2716219 -1.0736112 1.5702475 1.2947252
## hsa-mir-1193 hsa-mir-1197 hsa-mir-127 hsa-mir-134 hsa-mir-136
## 0.7893111 1.3379374 1.1731776 1.1993515 1.1603324
## hsa-mir-146a hsa-mir-154 hsa-mir-299 hsa-mir-323 hsa-mir-323b
## -0.7559942 1.2107862 1.1458929 1.2456081 1.2538499
## hsa-mir-329-1 hsa-mir-329-2 hsa-mir-337 hsa-mir-369 hsa-mir-370
## 1.4334220 1.4452910 1.0382505 1.1167849 1.2367825
## hsa-mir-376a-1 hsa-mir-376a-2 hsa-mir-376b hsa-mir-376c hsa-mir-377
## 1.2280260 1.3883613 1.1254736 1.1854181 1.2979233
## hsa-mir-379 hsa-mir-380 hsa-mir-381 hsa-mir-382 hsa-mir-409
## 1.1367002 1.4499531 1.1303332 1.1801769 1.1794923
## hsa-mir-410 hsa-mir-411 hsa-mir-412 hsa-mir-431 hsa-mir-432
## 1.1086159 1.3895000 0.9442754 1.0811420 1.1018494
## hsa-mir-433 hsa-mir-485 hsa-mir-487a hsa-mir-487b hsa-mir-489
## 1.2215302 1.3373563 1.5385568 1.1265769 -0.8030745
## hsa-mir-493 hsa-mir-494 hsa-mir-495 hsa-mir-496 hsa-mir-516a-2
## 0.8897820 1.3707919 1.0551570 1.1845408 -0.7887044
## hsa-mir-516b-1 hsa-mir-517a hsa-mir-518b hsa-mir-518f hsa-mir-539
## -0.7797897 -0.9432788 -0.9193731 -0.7734725 1.1034908
## hsa-mir-541 hsa-mir-543 hsa-mir-577 hsa-mir-605 hsa-mir-653
## 1.3977499 1.2640158 -0.8255819 -0.7621934 -0.7819097
## hsa-mir-654 hsa-mir-655 hsa-mir-656 hsa-mir-665 hsa-mir-668
## 1.1978980 1.4462898 1.7742395 1.2096247 1.3677798
## hsa-mir-758 hsa-mir-770 hsa-mir-876 hsa-mir-889
## 1.1177636 1.3295061 -0.8135486 1.1703091
##
## $`5bc`$bicluster5
## FASN.RPPA FN1.R2Gn CTNNB1.R2Gn CCND1.R2Gn hsa-mir-1258
## 0.7530785 0.7782749 0.9789055 0.9398745 -0.8778078
## hsa-mir-135b hsa-mir-2114 hsa-mir-3166 hsa-mir-3199-1 hsa-mir-3923
## 0.7789183 -0.9474872 0.8217578 -0.8002071 0.7653353
## hsa-mir-3926-2 hsa-mir-506 hsa-mir-507 hsa-mir-508 hsa-mir-509-1
## -0.8642790 -1.2810821 -1.5268068 -1.2511387 -1.2461806
## hsa-mir-509-2 hsa-mir-509-3 hsa-mir-510 hsa-mir-513a-1 hsa-mir-513a-2
## -1.2536204 -1.2361909 -1.6619289 -1.2442761 -1.3369888
## hsa-mir-513b hsa-mir-513c hsa-mir-514-1 hsa-mir-514-2 hsa-mir-514-3
## -1.1415689 -1.1019043 -1.2999527 -1.3123096 -1.3144639
## hsa-mir-514b
## -1.2016029
##
## $`5bc`$bicluster1
## G6PD.RPPA FASN.RPPA TSC1.RPPA TTF1.RPPA ERBB3.R2Gn
## -1.0238172 1.1176535 0.7533710 -0.9323751 0.8437467
## IGFBP2.R2Gn TGM2.R2Gn hsa-mir-1185-1 hsa-mir-1185-2 hsa-mir-1193
## 0.8312737 -0.9804476 1.2901309 1.0712054 0.9809614
## hsa-mir-1197 hsa-mir-1258 hsa-mir-127 hsa-mir-134 hsa-mir-136
## 1.1234606 -0.7732690 1.0133654 0.9826379 1.0258456
## hsa-mir-154 hsa-mir-2114 hsa-mir-299 hsa-mir-323 hsa-mir-323b
## 1.0244611 -0.8959236 0.9620621 1.0774052 1.0690317
## hsa-mir-329-1 hsa-mir-329-2 hsa-mir-337 hsa-mir-369 hsa-mir-370
## 1.2415553 1.4152582 1.0024046 0.9954036 1.0457143
## hsa-mir-376a-1 hsa-mir-376a-2 hsa-mir-376b hsa-mir-376c hsa-mir-377
## 1.1483753 1.0982166 1.0067403 0.9922984 1.0785131
## hsa-mir-379 hsa-mir-380 hsa-mir-381 hsa-mir-382 hsa-mir-3909
## 0.9567081 1.2575862 0.9574238 1.0033507 -0.7688510
## hsa-mir-3922 hsa-mir-409 hsa-mir-410 hsa-mir-411 hsa-mir-412
## -0.8133562 0.9986470 1.0242300 1.0572472 1.0263366
## hsa-mir-431 hsa-mir-432 hsa-mir-433 hsa-mir-466 hsa-mir-485
## 1.0854882 1.0919553 1.1385319 -1.1586721 1.0072154
## hsa-mir-487a hsa-mir-487b hsa-mir-493 hsa-mir-494 hsa-mir-495
## 1.2100117 1.0434050 0.9975330 1.0341061 0.9199375
## hsa-mir-496 hsa-mir-506 hsa-mir-507 hsa-mir-508 hsa-mir-509-1
## 1.0701750 -1.2031645 -1.3575097 -1.1717016 -1.0952425
## hsa-mir-509-2 hsa-mir-509-3 hsa-mir-510 hsa-mir-513a-1 hsa-mir-513a-2
## -1.1009373 -1.1005052 -1.5802550 -1.1577940 -1.2391731
## hsa-mir-513b hsa-mir-513c hsa-mir-514-1 hsa-mir-514-2 hsa-mir-514-3
## -1.0945976 -1.1089469 -1.1644768 -1.1737918 -1.1710175
## hsa-mir-514b hsa-mir-517a hsa-mir-539 hsa-mir-541 hsa-mir-543
## -1.0171652 -0.8674700 0.9944405 1.2455268 0.9873862
## hsa-mir-585 hsa-mir-605 hsa-mir-654 hsa-mir-655 hsa-mir-656
## -0.7452833 -0.8457441 1.0464010 1.1422255 1.4811616
## hsa-mir-665 hsa-mir-668 hsa-mir-758 hsa-mir-770 hsa-mir-889
## 1.1873457 1.1938936 0.9484045 1.2372062 1.0166875
##
## $`5bc`$bicluster4
## G6PD.RPPA IGFBP2.R2Gn FN1.R2Gn CCND1.R2Gn hsa-mir-1185-1
## -0.8874401 -0.7458151 -0.9565017 -0.8364112 0.9376338
## hsa-mir-1185-2 hsa-mir-1269 hsa-mir-2114 hsa-mir-3923 hsa-mir-411
## 0.7793299 -0.8862766 0.7511895 -0.9393513 0.8631381
## hsa-mir-485 hsa-mir-487a hsa-mir-494 hsa-mir-507 hsa-mir-509-2
## 0.8206766 0.8626403 0.7885223 0.8805492 0.7465243
## hsa-mir-510 hsa-mir-514-1 hsa-mir-514-2 hsa-mir-514-3 hsa-mir-543
## 1.0051334 0.7706746 0.7793074 0.7834490 0.7556145
## hsa-mir-655 hsa-mir-656
## 0.8555369 0.8747549
##
## $`5bc`$bicluster3
## TGM2.R2Gn hsa-mir-1185-1 hsa-mir-1185-2 hsa-mir-1197 hsa-mir-329-1
## -0.9917658 0.9119355 0.8179147 0.7677908 0.9301956
## hsa-mir-329-2 hsa-mir-380 hsa-mir-411 hsa-mir-485 hsa-mir-487a
## 0.8555830 0.7912598 0.8515268 0.7494611 0.8980823
## hsa-mir-494 hsa-mir-516a-1 hsa-mir-516a-2 hsa-mir-516b-1 hsa-mir-517a
## 0.7818349 -1.0238960 -0.8652304 -0.8930039 -1.1226980
## hsa-mir-518b hsa-mir-519a-2 hsa-mir-520a hsa-mir-541 hsa-mir-655
## -0.9249284 -0.7535023 -0.7649585 0.8239600 0.8520211
## hsa-mir-656 hsa-mir-668
## 1.0533879 0.8401613
##
##
## $`10bc`
## $`10bc`$bicluster9
## G6PD.RPPA BRCA2.RPPA FASN.RPPA INPP4B.RPPA TTF1.RPPA
## -1.4627449 -0.6720120 1.4086631 -0.9694645 -1.0291156
## VHL.RPPA PRDX1.RPPA G6PD.R2Gn MET.R2Gn FASN.R2Gn
## -0.8444524 -0.9069342 -0.7844535 -0.7018710 0.8476400
## TGM2.R2Gn PXN.R2Gn SQSTM1.R2Gn hsa-mir-1185-1 hsa-mir-1185-2
## -1.5283431 -0.8027402 -1.1032195 1.6309261 1.3876480
## hsa-mir-1193 hsa-mir-1197 hsa-mir-1258 hsa-mir-1269 hsa-mir-127
## 0.8020527 1.2937363 -0.8044344 -0.6902691 1.2667368
## hsa-mir-134 hsa-mir-136 hsa-mir-146a hsa-mir-153-1 hsa-mir-154
## 1.3017638 1.2877023 -0.8260444 0.6820200 1.3062989
## hsa-mir-196a-2 hsa-mir-205 hsa-mir-216b hsa-mir-224 hsa-mir-299
## 0.6992002 -0.6726063 -0.8044338 -0.6744452 1.2341408
## hsa-mir-323 hsa-mir-323b hsa-mir-329-1 hsa-mir-329-2 hsa-mir-337
## 1.3127688 1.3204813 1.5222314 1.6527292 1.1081292
## hsa-mir-369 hsa-mir-370 hsa-mir-376a-1 hsa-mir-376a-2 hsa-mir-376b
## 1.2098575 1.3405041 1.2791011 1.3927794 1.1857192
## hsa-mir-376c hsa-mir-377 hsa-mir-379 hsa-mir-380 hsa-mir-381
## 1.2531794 1.4120112 1.2195716 1.5192193 1.2101664
## hsa-mir-382 hsa-mir-409 hsa-mir-410 hsa-mir-411 hsa-mir-412
## 1.2535639 1.2593438 1.1442277 1.4901016 0.9761255
## hsa-mir-431 hsa-mir-432 hsa-mir-433 hsa-mir-452 hsa-mir-466
## 1.0949832 1.1301866 1.2224315 -0.7313466 -0.9866312
## hsa-mir-485 hsa-mir-487a hsa-mir-487b hsa-mir-489 hsa-mir-493
## 1.3799050 1.6292465 1.2048440 -0.9158299 0.8832365
## hsa-mir-494 hsa-mir-495 hsa-mir-496 hsa-mir-506 hsa-mir-507
## 1.4199328 1.1353186 1.2582445 -0.7289618 -0.7921094
## hsa-mir-508 hsa-mir-510 hsa-mir-513a-1 hsa-mir-513a-2 hsa-mir-513b
## -0.7055852 -1.0598608 -0.8244325 -0.7984791 -0.7538948
## hsa-mir-513c hsa-mir-514-1 hsa-mir-514-2 hsa-mir-516a-2 hsa-mir-517a
## -0.7275371 -0.6722299 -0.6769592 -0.7533639 -0.8643008
## hsa-mir-518b hsa-mir-518f hsa-mir-520a hsa-mir-539 hsa-mir-541
## -0.9086687 -0.7165163 -0.6894122 1.1965685 1.3723089
## hsa-mir-543 hsa-mir-548v hsa-mir-577 hsa-mir-605 hsa-mir-615
## 1.2839268 -0.8060584 -0.9002252 -0.8701715 0.7216102
## hsa-mir-653 hsa-mir-654 hsa-mir-655 hsa-mir-656 hsa-mir-665
## -0.8396767 1.2977646 1.5886964 1.8944918 1.4228691
## hsa-mir-668 hsa-mir-758 hsa-mir-770 hsa-mir-873 hsa-mir-876
## 1.3355796 1.1825793 1.4453960 -0.8171277 -1.2519276
## hsa-mir-889
## 1.2449389
##
## $`10bc`$bicluster10
## G6PD.RPPA RBM15.RPPA FASN.RPPA TSC1.RPPA TTF1.RPPA
## 0.7502456 -0.7800365 -1.5274105 -0.8180495 0.9069167
## VHL.RPPA AR.RPPA TFRC.RPPA AKT1S1.R2Gn IGFBP2.R2Gn
## 0.8539464 0.7157563 -0.8223625 -0.7682753 -0.8755194
## AKT2.R2Gn GATA3.R2Gn FASN.R2Gn CTNNB1.R2Gn TGM2.R2Gn
## -0.8230714 -0.6852798 -0.8902463 -0.8664015 0.6923561
## CCND1.R2Gn PIK3R1.R2Gn PXN.R2Gn RPTOR.R2Gn SQSTM1.R2Gn
## -0.7539605 0.8603335 0.7407626 -0.7716180 0.7578279
## hsa-mir-1185-1 hsa-mir-1193 hsa-mir-1197 hsa-mir-1258 hsa-mir-127
## -0.7455247 -0.8257255 -0.6908033 1.1115348 -0.7041091
## hsa-mir-1291 hsa-mir-134 hsa-mir-136 hsa-mir-154 hsa-mir-2114
## 0.8040902 -0.6912294 -0.7319809 -0.6972540 0.9960010
## hsa-mir-3166 hsa-mir-323 hsa-mir-323b hsa-mir-329-1 hsa-mir-329-2
## -0.7005083 -0.7205532 -0.6778538 -0.7892139 -1.1514295
## hsa-mir-337 hsa-mir-3655 hsa-mir-369 hsa-mir-370 hsa-mir-376a-1
## -0.7164329 0.6756809 -0.7181460 -0.7078798 -0.8083775
## hsa-mir-376a-2 hsa-mir-376b hsa-mir-377 hsa-mir-380 hsa-mir-382
## -0.7407880 -0.7184620 -0.7529196 -0.8568947 -0.6746157
## hsa-mir-3909 hsa-mir-3922 hsa-mir-3926-2 hsa-mir-410 hsa-mir-412
## 0.8736193 0.9005470 0.9053655 -0.7001987 -0.8014099
## hsa-mir-431 hsa-mir-432 hsa-mir-466 hsa-mir-487a hsa-mir-487b
## -0.7790305 -0.7756571 1.2096588 -0.7697183 -0.7303901
## hsa-mir-493 hsa-mir-496 hsa-mir-506 hsa-mir-507 hsa-mir-508
## -0.7359471 -0.7024296 1.4877862 1.6584772 1.4428013
## hsa-mir-509-1 hsa-mir-509-2 hsa-mir-509-3 hsa-mir-510 hsa-mir-513a-1
## 1.3927785 1.3999859 1.3987535 1.9970228 1.4671548
## hsa-mir-513a-2 hsa-mir-513b hsa-mir-513c hsa-mir-514-1 hsa-mir-514-2
## 1.5612417 1.3697259 1.3370295 1.4764641 1.4873631
## hsa-mir-514-3 hsa-mir-514b hsa-mir-539 hsa-mir-541 hsa-mir-552
## 1.4849702 1.2816265 -0.6982799 -0.7922268 0.6955907
## hsa-mir-585 hsa-mir-605 hsa-mir-615 hsa-mir-653 hsa-mir-654
## 0.6831848 1.1618128 -0.7770979 0.7249857 -0.7071541
## hsa-mir-655 hsa-mir-656 hsa-mir-665 hsa-mir-668 hsa-mir-770
## -0.7645098 -1.0122797 -0.9011850 -0.6794406 -0.9453659
## hsa-mir-876 hsa-mir-889 hsa-mir-891a
## 0.8334968 -0.6934538 0.6908017
##
## $`10bc`$bicluster7
## RBM15.RPPA GATA3.RPPA IGFBP2.R2Gn FN1.R2Gn GATA3.R2Gn
## 0.7563999 0.8045924 0.7044075 1.5105720 0.8053707
## CTNNB1.R2Gn CCND1.R2Gn hsa-mir-1185-1 hsa-mir-1185-2 hsa-mir-124-3
## 0.7888432 1.0074275 -0.8852070 -0.7269802 0.7182450
## hsa-mir-1269 hsa-mir-135b hsa-mir-206 hsa-mir-2114 hsa-mir-296
## 0.7423955 0.9636991 0.8609145 -1.0739371 -0.8379147
## hsa-mir-3144 hsa-mir-3166 hsa-mir-3199-1 hsa-mir-320c-2 hsa-mir-3655
## 0.7368974 0.8709674 -0.8448901 -0.7740326 -0.8200618
## hsa-mir-3923 hsa-mir-3926-2 hsa-mir-411 hsa-mir-429 hsa-mir-485
## 1.2458162 -0.7670181 -0.8065099 0.8136113 -0.7966192
## hsa-mir-487a hsa-mir-494 hsa-mir-506 hsa-mir-507 hsa-mir-508
## -0.7572892 -0.6984286 -1.1966336 -1.5059972 -1.1635007
## hsa-mir-509-1 hsa-mir-509-2 hsa-mir-509-3 hsa-mir-510 hsa-mir-513a-1
## -1.1993246 -1.2090071 -1.1840188 -1.5948701 -1.1167460
## hsa-mir-513a-2 hsa-mir-513b hsa-mir-513c hsa-mir-514-1 hsa-mir-514-2
## -1.2067379 -1.0652999 -1.0159501 -1.2219215 -1.2360464
## hsa-mir-514-3 hsa-mir-514b hsa-mir-543 hsa-mir-548q hsa-mir-582
## -1.2408427 -1.1833782 -0.7327624 -0.6799517 0.7057430
## hsa-mir-655 hsa-mir-656
## -0.7380438 -0.7860848
##
## $`10bc`$bicluster2
## G6PD.RPPA GATA3.RPPA G6PD.R2Gn FN1.R2Gn CTNNB1.R2Gn
## -1.0324020 -0.7398528 -0.7652069 -0.7904096 -0.7320277
## TGM2.R2Gn CCND1.R2Gn hsa-mir-1185-1 hsa-mir-1185-2 hsa-mir-1197
## -0.8680783 -0.7788517 1.5722839 1.2743358 1.2771463
## hsa-mir-127 hsa-mir-134 hsa-mir-136 hsa-mir-154 hsa-mir-206
## 1.0692791 1.0811956 1.0507731 1.1280179 -0.9939034
## hsa-mir-299 hsa-mir-3193 hsa-mir-3199-1 hsa-mir-323 hsa-mir-323b
## 1.0391293 -0.6877791 0.7759127 1.1607170 1.1948102
## hsa-mir-329-1 hsa-mir-329-2 hsa-mir-337 hsa-mir-369 hsa-mir-370
## 1.3168450 1.1471794 0.9078835 0.9956719 1.1286636
## hsa-mir-376a-1 hsa-mir-376a-2 hsa-mir-376b hsa-mir-376c hsa-mir-377
## 1.1252145 1.2781860 0.9979647 1.0881306 1.2012004
## hsa-mir-379 hsa-mir-380 hsa-mir-381 hsa-mir-382 hsa-mir-409
## 1.0254371 1.3078617 1.0076786 1.1057500 1.0817756
## hsa-mir-410 hsa-mir-411 hsa-mir-412 hsa-mir-431 hsa-mir-432
## 1.0059600 1.3517763 0.7848014 0.9465402 0.9652966
## hsa-mir-433 hsa-mir-485 hsa-mir-487a hsa-mir-487b hsa-mir-493
## 1.1829576 1.3365774 1.4623399 1.0189098 0.7628048
## hsa-mir-494 hsa-mir-495 hsa-mir-496 hsa-mir-516a-2 hsa-mir-516b-1
## 1.3256351 0.9670353 1.1038734 -0.7677328 -0.6735615
## hsa-mir-517a hsa-mir-518b hsa-mir-518c hsa-mir-518f hsa-mir-520a
## -1.0245409 -0.8109733 -0.6788923 -0.7513600 -0.7589637
## hsa-mir-526b hsa-mir-539 hsa-mir-541 hsa-mir-543 hsa-mir-577
## -0.7156342 1.0002474 1.3104107 1.2778057 -0.7900686
## hsa-mir-580 hsa-mir-654 hsa-mir-655 hsa-mir-656 hsa-mir-665
## 0.6758842 1.0956032 1.3401407 1.6811212 0.9901515
## hsa-mir-668 hsa-mir-758 hsa-mir-770 hsa-mir-889
## 1.3754313 1.0163034 1.1315742 1.0784478
##
## $`10bc`$bicluster1
## G6PD.RPPA FN1.R2Gn TGM2.R2Gn hsa-mir-1185-1 hsa-mir-1185-2
## -0.8751739 -0.9547080 -0.7701581 1.2875673 1.0640023
## hsa-mir-1197 hsa-mir-127 hsa-mir-134 hsa-mir-136 hsa-mir-154
## 0.9647186 0.9416451 0.9477569 0.9450738 0.9481687
## hsa-mir-299 hsa-mir-323 hsa-mir-323b hsa-mir-329-1 hsa-mir-329-2
## 0.8898955 0.9558071 1.0119887 1.0574270 1.0611295
## hsa-mir-337 hsa-mir-369 hsa-mir-370 hsa-mir-376a-1 hsa-mir-376a-2
## 0.7826329 0.8720431 0.9593036 0.9414308 1.0470675
## hsa-mir-376b hsa-mir-376c hsa-mir-377 hsa-mir-379 hsa-mir-380
## 0.8579101 0.8943005 0.9395190 0.8850704 1.1203452
## hsa-mir-381 hsa-mir-382 hsa-mir-409 hsa-mir-410 hsa-mir-411
## 0.8668566 0.8992530 0.9242129 0.8482490 1.1144084
## hsa-mir-412 hsa-mir-431 hsa-mir-432 hsa-mir-433 hsa-mir-485
## 0.7347550 0.8128670 0.8206149 1.0782266 1.0886604
## hsa-mir-487a hsa-mir-487b hsa-mir-494 hsa-mir-495 hsa-mir-496
## 1.2093248 0.8838277 1.0174403 0.7871374 0.9098792
## hsa-mir-539 hsa-mir-541 hsa-mir-543 hsa-mir-654 hsa-mir-655
## 0.8638615 1.0520097 1.0151944 0.9399797 1.1057531
## hsa-mir-656 hsa-mir-665 hsa-mir-668 hsa-mir-758 hsa-mir-770
## 1.3345000 0.9436418 1.0677259 0.8597992 0.9978195
## hsa-mir-889
## 0.8845916
##
## $`10bc`$bicluster3
## TGM2.R2Gn hsa-mir-1185-1 hsa-mir-329-1 hsa-mir-329-2 hsa-mir-506
## -0.7815945 0.6713936 0.7096430 0.7284656 -0.6827509
## hsa-mir-507 hsa-mir-508 hsa-mir-510 hsa-mir-513a-1 hsa-mir-513a-2
## -0.7432906 -0.7058996 -0.9944091 -0.7219759 -0.7453797
## hsa-mir-513c hsa-mir-514b hsa-mir-516b-1 hsa-mir-517a hsa-mir-518b
## -0.6759318 -0.6772861 -0.7750374 -0.8073668 -0.8075451
## hsa-mir-656
## 0.8191651
##
## $`10bc`$bicluster8
## G6PD.RPPA ERBB3.R2Gn TGM2.R2Gn hsa-mir-1185-1 hsa-mir-1185-2
## -0.8578145 1.0985669 -0.7422173 1.0497708 0.8854318
## hsa-mir-1197 hsa-mir-1269 hsa-mir-127 hsa-mir-134 hsa-mir-136
## 0.7948017 -0.6893234 0.7122095 0.6782873 0.7426809
## hsa-mir-154 hsa-mir-206 hsa-mir-299 hsa-mir-323 hsa-mir-323b
## 0.7654090 -0.6895200 0.6903261 0.7785561 0.8043037
## hsa-mir-329-1 hsa-mir-329-2 hsa-mir-369 hsa-mir-370 hsa-mir-376a-1
## 0.8900127 0.8349306 0.6725965 0.7575411 0.7445226
## hsa-mir-376a-2 hsa-mir-376b hsa-mir-376c hsa-mir-377 hsa-mir-379
## 0.7800835 0.6753648 0.7185616 0.8123670 0.6821885
## hsa-mir-380 hsa-mir-381 hsa-mir-382 hsa-mir-409 hsa-mir-410
## 0.8673392 0.6966778 0.7274808 0.7332409 0.7066824
## hsa-mir-411 hsa-mir-432 hsa-mir-433 hsa-mir-485 hsa-mir-487a
## 0.8832058 0.6874621 0.8246066 0.8393091 0.9210298
## hsa-mir-487b hsa-mir-494 hsa-mir-496 hsa-mir-517a hsa-mir-539
## 0.7299098 0.8012510 0.8134274 -0.9384336 0.7091134
## hsa-mir-541 hsa-mir-543 hsa-mir-654 hsa-mir-655 hsa-mir-656
## 0.8027538 0.8393921 0.7468551 0.8661148 1.1191052
## hsa-mir-665 hsa-mir-668 hsa-mir-758 hsa-mir-770 hsa-mir-889
## 0.7904591 0.8699738 0.6758522 0.7341120 0.7577327
##
## $`10bc`$bicluster6
## FASN.RPPA hsa-mir-3934 hsa-mir-466 hsa-mir-510 hsa-mir-605
## 0.9751094 -0.7307437 -0.7125538 -0.7708856 -0.8211215
##
## $`10bc`$bicluster5
## named numeric(0)
##
## $`10bc`$bicluster4
## G6PD.RPPA
## -0.86336671. Convert microRNA to genes
Also remove the ending “.R2Gn” and “.RPPA” from gene names.
split.by.omic = function(variable.list) {
out.mRSG = variable.list[startsWith(variable.list, "hsa")]
out.R2Gn = variable.list[endsWith(variable.list, ".R2Gn")]
out.RPPA = variable.list[endsWith(variable.list, ".RPPA")]
out = list("miRNASeqGene" = out.mRSG,
"RNASeq2GeneNorm" = out.R2Gn,
"RPPAArray" = out.RPPA)
out
}multiomics.to.GENES = function(sel.features, full.search = F, table = "validated", drop.miRNA = F) {
multiomics.list = split.by.omic(sel.features)
# Convert miRNASeqGene to target GENE names
# Skipped and returns an empty list instead of the list of select features,
# or if microRNA features are explicitly dropped (drop.miRNA = T).
# (Usually done when the features has only a few miRNA and unable to target any genes)
if (length(multiomics.list[[1]]) > 0 & !drop.miRNA) {
if (!full.search) { # Search only among the 198 genes in ACC, recommended
targets= get_multimir(mirna = multiomics.list[[1]],
target = gene.names,
table = table,
summary = T)
mRSG.target.genes = unique(targets@data$target_symbol)
} else { # Search the full dataset, not recommended.
# Use only if ACC gene search returns nothing or fails.
# Genes not in the ACC genes need to be manually removed.
targets= get_multimir(mirna = multiomics.list[[1]],
table = table,
summary = T)
mRSG.target.genes = unique(targets@data$target_symbol)
}
} else {
mRSG.target.genes = list()
}
#Remove suffix for Pathway Analysis Compatibility
R2Gn.genes = str_remove(multiomics.list[[2]], ".R2Gn")
RPPA.genes = str_remove(multiomics.list[[3]], ".RPPA")
#Join all cleaned-up genes are remove duplicates.
out1 = c(mRSG.target.genes, R2Gn.genes, RPPA.genes)
out = as.character(unique(out1))
out
}geneNames <- list("Factor1of1"= multiomics.to.GENES(names(sel.features$`1bc`$bicluster1)),
"Factor1of2"= multiomics.to.GENES(names(sel.features$`2bc`$bicluster1)),
"Factor2of2"= multiomics.to.GENES(names(sel.features$`2bc`$bicluster2)),
"Factor1of3"= multiomics.to.GENES(names(sel.features$`3bc`$bicluster1)),
"Factor2of3"= multiomics.to.GENES(names(sel.features$`3bc`$bicluster2)),
"Factor3of3"= multiomics.to.GENES(names(sel.features$`3bc`$bicluster3)),
"Factor1of5"= multiomics.to.GENES(names(sel.features$`5bc`$bicluster1)),
"Factor2of5"= multiomics.to.GENES(names(sel.features$`5bc`$bicluster2)),
"Factor3of5"= multiomics.to.GENES(names(sel.features$`5bc`$bicluster3)),
"Factor4of5"= multiomics.to.GENES(names(sel.features$`5bc`$bicluster4)),
"Factor5of5"= multiomics.to.GENES(names(sel.features$`5bc`$bicluster5)),
"Factor1of10"= multiomics.to.GENES(names(sel.features$`10bc`$bicluster1)),
"Factor2of10"= multiomics.to.GENES(names(sel.features$`10bc`$bicluster2)),
"Factor3of10"= multiomics.to.GENES(names(sel.features$`10bc`$bicluster3)),
"Factor4of10"= multiomics.to.GENES(names(sel.features$`10bc`$bicluster4)),
"Factor5of10"= multiomics.to.GENES(names(sel.features$`10bc`$bicluster5)), #Empty
"Factor6of10"= multiomics.to.GENES(names(sel.features$`10bc`$bicluster6)),
"Factor7of10"= multiomics.to.GENES(names(sel.features$`10bc`$bicluster7)),
"Factor8of10"= multiomics.to.GENES(names(sel.features$`10bc`$bicluster8)),
"Factor9of10"= multiomics.to.GENES(names(sel.features$`10bc`$bicluster9)),
"Factor10of10"= multiomics.to.GENES(names(sel.features$`10bc`$bicluster10))
)## Searching mirecords ...
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## Searching tarbase ...geneNames## $Factor1of1
## [1] "HSPA1A" "AKT1" "VHL" "MTOR" "MAPK8" "MYH9" "CDKN1A" "FOXO3"
## [9] "ATM" "CASP8" "MACC1" "PTEN" "KRAS" "NRAS" "PTK2" "ETS1"
## [17] "STAT5A" "CCND1" "YAP1" "ITGA2" "MAPK1" "ANLN" "TGM2" "G6PD"
##
## $Factor1of2
## [1] "ESR1" "MET" "G6PD" "BCL2" "KRAS" "CCND1" "NOTCH3" "AKT1"
## [9] "IGF1R" "ETS1" "XIAP" "MAPK8" "ARID1A" "BID" "PTEN" "NRAS"
## [17] "PTK2" "ATM" "YWHAZ" "FOXO3" "CHEK1" "FN1" "NCOA3" "GAB2"
## [25] "ITGA2" "CTNNB1"
##
## $Factor2of2
## [1] "RB1" "XIAP" "HSPA1A" "AKT1" "VHL" "MTOR" "MAPK8" "ETS1"
## [9] "ARID1A" "BID" "MYH9" "CDKN1A" "FOXO3" "ATM" "CASP8" "MACC1"
## [17] "PTEN" "KRAS" "NRAS" "PTK2" "CCND1" "PIK3R1" "CHEK1" "IGF1R"
## [25] "SRSF1" "TUBA1B" "STAT5A" "NCOA3" "YAP1" "ITGA2" "MAPK1" "GAB2"
## [33] "ANLN" "TGM2" "SQSTM1" "G6PD" "RBM15" "FASN" "TTF1"
##
## $Factor1of3
## [1] "ESR1" "MET" "G6PD" "BCL2" "KRAS" "CCND1" "NOTCH3"
## [8] "AKT1" "IGF1R" "HSPA1A" "VHL" "MTOR" "MAPK8" "MYH9"
## [15] "CDKN1A" "FOXO3" "ATM" "CASP8" "MACC1" "PTEN" "NRAS"
## [22] "PTK2" "ETS1" "PARP1" "CCNE2" "RAB25" "YWHAZ" "STAT5A"
## [29] "MYC" "CASP3" "BCL2L11" "YAP1" "CHEK1" "FN1" "MSH6"
## [36] "ITGA2" "PIK3CA" "MAPK1" "SRSF1" "ANLN" "ERBB3" "CDH2"
## [43] "CTNNB1" "TGM2"
##
## $Factor2of3
## [1] "ETS1" "XIAP" "MAPK8" "ARID1A" "BID" "MYH9" "CDKN1A" "FOXO3"
## [9] "ATM" "CASP8" "MACC1" "CCND1" "PIK3R1" "CHEK1" "IGF1R" "SRSF1"
## [17] "TUBA1B" "STAT5A" "NCOA3" "GAB2" "YAP1" "MAPK1" "ANLN" "TGM2"
## [25] "G6PD" "FASN"
##
## $Factor3of3
## [1] "ESR1" "MET" "G6PD" "BCL2" "KRAS" "CCND1" "NOTCH3" "AKT1"
## [9] "IGF1R" "ETS1" "XIAP" "MAPK8" "ARID1A" "BID" "YWHAZ" "FOXO3"
## [17] "CHEK1" "FN1" "NCOA3" "GAB2" "IGFBP2" "CTNNB1" "GATA3"
##
## $Factor1of5
## [1] "RB1" "XIAP" "HSPA1A" "AKT1" "VHL" "MTOR" "MAPK8" "ETS1"
## [9] "ARID1A" "BID" "MYH9" "CDKN1A" "FOXO3" "ATM" "CASP8" "MACC1"
## [17] "PTEN" "KRAS" "NRAS" "PTK2" "CCND1" "PIK3R1" "CHEK1" "IGF1R"
## [25] "SRSF1" "TUBA1B" "STAT5A" "NCOA3" "YAP1" "ITGA2" "MAPK1" "GAB2"
## [33] "ANLN" "ERBB3" "IGFBP2" "TGM2" "G6PD" "FASN" "TSC1" "TTF1"
##
## $Factor2of5
## [1] "HSPA1A" "AKT1" "VHL" "MTOR" "MAPK8" "MYH9" "CDKN1A"
## [8] "FOXO3" "ATM" "CASP8" "MACC1" "PTEN" "KRAS" "NRAS"
## [15] "PTK2" "ETS1" "PARP1" "IGF1R" "CCNE2" "RAB25" "CCND1"
## [22] "XIAP" "STAT5A" "BCL2" "MYC" "CASP3" "BCL2L11" "YAP1"
## [29] "MSH6" "ITGA2" "PIK3CA" "MAPK1" "SRSF1" "ANLN" "G6PD"
## [36] "TGM2" "SQSTM1" "FASN" "INPP4B" "TTF1" "PRDX1"
##
## $Factor3of5
## [1] "CDKN1A" "STAT5A" "TGM2"
##
## $Factor4of5
## [1] "ETS1" "XIAP" "MAPK8" "ARID1A" "BID" "PTEN" "KRAS" "NRAS"
## [9] "PTK2" "ATM" "NCOA3" "GAB2" "ITGA2" "IGFBP2" "FN1" "CCND1"
## [17] "G6PD"
##
## $Factor5of5
## [1] "RB1" "XIAP" "ETS1" "MAPK8" "ARID1A" "BID" "YWHAZ" "NCOA3"
## [9] "GAB2" "FN1" "CTNNB1" "CCND1" "FASN"
##
## $Factor1of10
## [1] "HSPA1A" "AKT1" "VHL" "MTOR" "MAPK8" "MYH9" "CDKN1A" "FOXO3"
## [9] "ATM" "CASP8" "MACC1" "PTEN" "KRAS" "NRAS" "PTK2" "ETS1"
## [17] "STAT5A" "CCND1" "YAP1" "ITGA2" "MAPK1" "ANLN" "FN1" "TGM2"
## [25] "G6PD"
##
## $Factor2of10
## [1] "ESR1" "MET" "G6PD" "BCL2" "KRAS" "CCND1" "NOTCH3"
## [8] "AKT1" "IGF1R" "HSPA1A" "VHL" "MTOR" "MAPK8" "MYH9"
## [15] "CDKN1A" "FOXO3" "ATM" "CASP8" "MACC1" "PTEN" "NRAS"
## [22] "PTK2" "ETS1" "PARP1" "CCNE2" "RAB25" "STAT5A" "MYC"
## [29] "CASP3" "BCL2L11" "YAP1" "CHEK1" "FN1" "MSH6" "ITGA2"
## [36] "PIK3CA" "MAPK1" "SRSF1" "ANLN" "CTNNB1" "TGM2" "GATA3"
##
## $Factor3of10
## [1] "ETS1" "XIAP" "MAPK8" "ARID1A" "BID" "NCOA3" "GAB2" "TGM2"
##
## $Factor4of10
## [1] "G6PD"
##
## $Factor5of10
## character(0)
##
## $Factor6of10
## [1] "CCND1" "PIK3R1" "XIAP" "CHEK1" "IGF1R" "SRSF1" "TUBA1B" "FASN"
##
## $Factor7of10
## [1] "ESR1" "MET" "BAP1" "ERRFI1" "G6PD" "BCL2" "KRAS"
## [8] "CCND1" "NOTCH3" "AKT1" "IGF1R" "PTEN" "CDKN1B" "IRS1"
## [15] "MYC" "JUN" "BCL2L11" "EZH2" "SHC1" "XIAP" "ETS1"
## [22] "MAPK8" "ARID1A" "BID" "NRAS" "PTK2" "ATM" "YWHAZ"
## [29] "MAPT" "CHEK2" "NCOA3" "AXL" "CDKN1A" "EGFR" "CAV1"
## [36] "CASP3" "ANXA1" "TFF1" "FOXO3" "STAT3" "ASNS" "CHEK1"
## [43] "FOXM1" "FN1" "IGFBP2" "ITGA2" "RET" "SQSTM1" "CCNE2"
## [50] "GAB2" "NDRG1" "INPP4B" "LCN2" "RAD50" "GATA3" "CTNNB1"
## [57] "RBM15"
##
## $Factor8of10
## [1] "ESR1" "MET" "G6PD" "BCL2" "KRAS" "CCND1" "NOTCH3" "AKT1"
## [9] "IGF1R" "HSPA1A" "VHL" "MTOR" "MAPK8" "MYH9" "CDKN1A" "FOXO3"
## [17] "ATM" "CASP8" "MACC1" "PTEN" "NRAS" "PTK2" "ETS1" "STAT5A"
## [25] "YAP1" "CHEK1" "FN1" "ITGA2" "MAPK1" "ANLN" "ERBB3" "TGM2"
##
## $Factor9of10
## [1] "RB1" "XIAP" "HSPA1A" "AKT1" "VHL" "MTOR" "MAPK8"
## [8] "ETS1" "ARID1A" "BID" "MYH9" "CDKN1A" "FOXO3" "ATM"
## [15] "CASP8" "MACC1" "PTEN" "KRAS" "NRAS" "PTK2" "PARP1"
## [22] "IGF1R" "CCNE2" "RAB25" "CCND1" "PIK3R1" "CHEK1" "SRSF1"
## [29] "TUBA1B" "STAT5A" "CDKN1B" "BCL2L11" "BCL2" "NCOA3" "MYC"
## [36] "CASP3" "YAP1" "MSH6" "ITGA2" "PIK3CA" "MAPK1" "GAB2"
## [43] "ANLN" "G6PD" "MET" "FASN" "TGM2" "PXN" "SQSTM1"
## [50] "BRCA2" "INPP4B" "TTF1" "PRDX1"
##
## $Factor10of10
## [1] "RB1" "XIAP" "HSPA1A" "AKT1" "VHL" "MTOR" "MAPK8" "ETS1"
## [9] "ARID1A" "BID" "MYH9" "CDKN1A" "FOXO3" "ATM" "CASP8" "MACC1"
## [17] "YWHAZ" "CCND1" "PIK3R1" "CHEK1" "IGF1R" "SRSF1" "TUBA1B" "NRAS"
## [25] "STAT5A" "PTEN" "NCOA3" "E2F1" "CASP9" "CDKN2A" "CCNE1" "MAPK9"
## [33] "RAF1" "AKT2" "YAP1" "BCL2L1" "DVL3" "SMAD3" "PRKCA" "MAPK1"
## [41] "MAPK3" "GAB2" "ANLN" "AKT1S1" "IGFBP2" "GATA3" "FASN" "CTNNB1"
## [49] "TGM2" "PXN" "RPTOR" "SQSTM1" "G6PD" "RBM15" "TSC1" "TTF1"
## [57] "AR" "TFRC"saveRDS(geneNames, file = "data/sel_features/gene_converted/genes_fabia_extracted_by_bic.rds")2. Pathway Analysis
A. GO Classification
ggo_MF <- list()#functional profile of a geneset for Molecular Function
ggo_BP <- list()#functional profile of a geneset for Biological Process
ggo_CC <- list()#functional profile of a geneset for Cellular Component
for(z in 1:length(geneNames)){
print(z)
input <- geneNames[[z]]
ggo_MF[[z]] <- groupGO(gene=input,
OrgDb = org.Hs.eg.db,
ont="MF",
keyType="SYMBOL",
readable=TRUE)
ggo_BP[[z]] <- groupGO(gene=input,
OrgDb = org.Hs.eg.db,
ont="BP",
keyType="SYMBOL",
readable=TRUE)
ggo_CC[[z]] <- groupGO(gene=input,
OrgDb = org.Hs.eg.db,
ont="CC",
keyType="SYMBOL",
readable=TRUE)
}## [1] 1
## [1] 2
## [1] 3
## [1] 4
## [1] 5
## [1] 6
## [1] 7
## [1] 8
## [1] 9
## [1] 10
## [1] 11
## [1] 12
## [1] 13
## [1] 14
## [1] 15
## [1] 16
## [1] 17
## [1] 18
## [1] 19
## [1] 20
## [1] 21for(z in 1:length(geneNames)) {
print(head(ggo_MF[[z]]))
print(head(ggo_BP[[z]]))
print(head(ggo_CC[[z]]))
}## ID Description Count GeneRatio
## GO:0003774 GO:0003774 cytoskeletal motor activity 1 1/24
## GO:0003824 GO:0003824 catalytic activity 16 16/24
## GO:0005198 GO:0005198 structural molecule activity 0 0/24
## GO:0005215 GO:0005215 transporter activity 0 0/24
## GO:0005488 GO:0005488 binding 24 24/24
## GO:0009055 GO:0009055 electron transfer activity 0 0/24
## geneID
## GO:0003774 MYH9
## GO:0003824 HSPA1A/AKT1/VHL/MTOR/MAPK8/CDKN1A/ATM/CASP8/PTEN/KRAS/NRAS/PTK2/CCND1/MAPK1/TGM2/G6PD
## GO:0005198
## GO:0005215
## GO:0005488 HSPA1A/AKT1/VHL/MTOR/MAPK8/MYH9/CDKN1A/FOXO3/ATM/CASP8/MACC1/PTEN/KRAS/NRAS/PTK2/ETS1/STAT5A/CCND1/YAP1/ITGA2/MAPK1/ANLN/TGM2/G6PD
## GO:0009055
## ID Description Count GeneRatio
## GO:0000003 GO:0000003 reproduction 8 8/24
## GO:0002376 GO:0002376 immune system process 14 14/24
## GO:0008152 GO:0008152 metabolic process 22 22/24
## GO:0009987 GO:0009987 cellular process 24 24/24
## GO:0016032 GO:0016032 viral process 3 3/24
## GO:0022414 GO:0022414 reproductive process 8 8/24
## geneID
## GO:0000003 AKT1/MTOR/MYH9/FOXO3/ATM/CASP8/PTEN/ITGA2
## GO:0002376 HSPA1A/AKT1/MTOR/MAPK8/MYH9/CDKN1A/FOXO3/ATM/CASP8/PTK2/ETS1/ITGA2/MAPK1/G6PD
## GO:0008152 HSPA1A/AKT1/VHL/MTOR/MAPK8/MYH9/CDKN1A/FOXO3/ATM/CASP8/MACC1/PTEN/KRAS/PTK2/ETS1/STAT5A/CCND1/YAP1/ITGA2/MAPK1/TGM2/G6PD
## GO:0009987 HSPA1A/AKT1/VHL/MTOR/MAPK8/MYH9/CDKN1A/FOXO3/ATM/CASP8/MACC1/PTEN/KRAS/NRAS/PTK2/ETS1/STAT5A/CCND1/YAP1/ITGA2/MAPK1/ANLN/TGM2/G6PD
## GO:0016032 HSPA1A/AKT1/ITGA2
## GO:0022414 AKT1/MTOR/MYH9/FOXO3/ATM/CASP8/PTEN/ITGA2
## ID Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex 14 14/24
## GO:0044423 GO:0044423 virion component 0 0/24
## GO:0110165 GO:0110165 cellular anatomical entity 24 24/24
## geneID
## GO:0032991 HSPA1A/AKT1/MTOR/MYH9/CDKN1A/FOXO3/ATM/CASP8/ETS1/STAT5A/CCND1/YAP1/ITGA2/TGM2
## GO:0044423
## GO:0110165 HSPA1A/AKT1/VHL/MTOR/MAPK8/MYH9/CDKN1A/FOXO3/ATM/CASP8/MACC1/PTEN/KRAS/NRAS/PTK2/ETS1/STAT5A/CCND1/YAP1/ITGA2/MAPK1/ANLN/TGM2/G6PD
## ID Description Count GeneRatio
## GO:0003774 GO:0003774 cytoskeletal motor activity 0 0/26
## GO:0003824 GO:0003824 catalytic activity 14 14/26
## GO:0005198 GO:0005198 structural molecule activity 1 1/26
## GO:0005215 GO:0005215 transporter activity 2 2/26
## GO:0005488 GO:0005488 binding 26 26/26
## GO:0009055 GO:0009055 electron transfer activity 0 0/26
## geneID
## GO:0003774
## GO:0003824 MET/G6PD/KRAS/CCND1/AKT1/IGF1R/XIAP/MAPK8/PTEN/NRAS/PTK2/ATM/CHEK1/NCOA3
## GO:0005198 FN1
## GO:0005215 BCL2/IGF1R
## GO:0005488 ESR1/MET/G6PD/BCL2/KRAS/CCND1/NOTCH3/AKT1/IGF1R/ETS1/XIAP/MAPK8/ARID1A/BID/PTEN/NRAS/PTK2/ATM/YWHAZ/FOXO3/CHEK1/FN1/NCOA3/GAB2/ITGA2/CTNNB1
## GO:0009055
## ID Description Count GeneRatio
## GO:0000003 GO:0000003 reproduction 9 9/26
## GO:0002376 GO:0002376 immune system process 18 18/26
## GO:0008152 GO:0008152 metabolic process 24 24/26
## GO:0009987 GO:0009987 cellular process 26 26/26
## GO:0016032 GO:0016032 viral process 3 3/26
## GO:0022414 GO:0022414 reproductive process 9 9/26
## geneID
## GO:0000003 ESR1/BCL2/AKT1/IGF1R/PTEN/ATM/FOXO3/ITGA2/CTNNB1
## GO:0002376 ESR1/G6PD/BCL2/AKT1/IGF1R/ETS1/XIAP/MAPK8/ARID1A/BID/PTK2/ATM/YWHAZ/FOXO3/FN1/GAB2/ITGA2/CTNNB1
## GO:0008152 ESR1/MET/G6PD/BCL2/KRAS/CCND1/NOTCH3/AKT1/IGF1R/ETS1/XIAP/MAPK8/ARID1A/BID/PTEN/PTK2/ATM/YWHAZ/FOXO3/CHEK1/FN1/NCOA3/ITGA2/CTNNB1
## GO:0009987 ESR1/MET/G6PD/BCL2/KRAS/CCND1/NOTCH3/AKT1/IGF1R/ETS1/XIAP/MAPK8/ARID1A/BID/PTEN/NRAS/PTK2/ATM/YWHAZ/FOXO3/CHEK1/FN1/NCOA3/GAB2/ITGA2/CTNNB1
## GO:0016032 BCL2/AKT1/ITGA2
## GO:0022414 ESR1/BCL2/AKT1/IGF1R/PTEN/ATM/FOXO3/ITGA2/CTNNB1
## ID Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex 16 16/26
## GO:0044423 GO:0044423 virion component 0 0/26
## GO:0110165 GO:0110165 cellular anatomical entity 26 26/26
## geneID
## GO:0032991 ESR1/MET/BCL2/CCND1/NOTCH3/AKT1/IGF1R/ETS1/ARID1A/ATM/FOXO3/CHEK1/FN1/NCOA3/ITGA2/CTNNB1
## GO:0044423
## GO:0110165 ESR1/MET/G6PD/BCL2/KRAS/CCND1/NOTCH3/AKT1/IGF1R/ETS1/XIAP/MAPK8/ARID1A/BID/PTEN/NRAS/PTK2/ATM/YWHAZ/FOXO3/CHEK1/FN1/NCOA3/GAB2/ITGA2/CTNNB1
## ID Description Count GeneRatio
## GO:0003774 GO:0003774 cytoskeletal motor activity 1 1/39
## GO:0003824 GO:0003824 catalytic activity 23 23/39
## GO:0005198 GO:0005198 structural molecule activity 1 1/39
## GO:0005215 GO:0005215 transporter activity 1 1/39
## GO:0005488 GO:0005488 binding 39 39/39
## GO:0009055 GO:0009055 electron transfer activity 0 0/39
## geneID
## GO:0003774 MYH9
## GO:0003824 XIAP/HSPA1A/AKT1/VHL/MTOR/MAPK8/CDKN1A/ATM/CASP8/PTEN/KRAS/NRAS/PTK2/CCND1/PIK3R1/CHEK1/IGF1R/TUBA1B/NCOA3/MAPK1/TGM2/G6PD/FASN
## GO:0005198 TUBA1B
## GO:0005215 IGF1R
## GO:0005488 RB1/XIAP/HSPA1A/AKT1/VHL/MTOR/MAPK8/ETS1/ARID1A/BID/MYH9/CDKN1A/FOXO3/ATM/CASP8/MACC1/PTEN/KRAS/NRAS/PTK2/CCND1/PIK3R1/CHEK1/IGF1R/SRSF1/TUBA1B/STAT5A/NCOA3/YAP1/ITGA2/MAPK1/GAB2/ANLN/TGM2/SQSTM1/G6PD/RBM15/FASN/TTF1
## GO:0009055
## ID Description Count GeneRatio
## GO:0000003 GO:0000003 reproduction 10 10/39
## GO:0002376 GO:0002376 immune system process 23 23/39
## GO:0008152 GO:0008152 metabolic process 35 35/39
## GO:0009987 GO:0009987 cellular process 39 39/39
## GO:0016032 GO:0016032 viral process 3 3/39
## GO:0022414 GO:0022414 reproductive process 10 10/39
## geneID
## GO:0000003 RB1/AKT1/MTOR/MYH9/FOXO3/ATM/CASP8/PTEN/IGF1R/ITGA2
## GO:0002376 RB1/XIAP/HSPA1A/AKT1/MTOR/MAPK8/ETS1/ARID1A/BID/MYH9/CDKN1A/FOXO3/ATM/CASP8/PTK2/PIK3R1/IGF1R/ITGA2/MAPK1/GAB2/SQSTM1/G6PD/RBM15
## GO:0008152 RB1/XIAP/HSPA1A/AKT1/VHL/MTOR/MAPK8/ETS1/ARID1A/BID/MYH9/CDKN1A/FOXO3/ATM/CASP8/MACC1/PTEN/KRAS/PTK2/CCND1/PIK3R1/CHEK1/IGF1R/SRSF1/STAT5A/NCOA3/YAP1/ITGA2/MAPK1/TGM2/SQSTM1/G6PD/RBM15/FASN/TTF1
## GO:0009987 RB1/XIAP/HSPA1A/AKT1/VHL/MTOR/MAPK8/ETS1/ARID1A/BID/MYH9/CDKN1A/FOXO3/ATM/CASP8/MACC1/PTEN/KRAS/NRAS/PTK2/CCND1/PIK3R1/CHEK1/IGF1R/SRSF1/TUBA1B/STAT5A/NCOA3/YAP1/ITGA2/MAPK1/GAB2/ANLN/TGM2/SQSTM1/G6PD/RBM15/FASN/TTF1
## GO:0016032 HSPA1A/AKT1/ITGA2
## GO:0022414 RB1/AKT1/MTOR/MYH9/FOXO3/ATM/CASP8/PTEN/IGF1R/ITGA2
## ID Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex 22 22/39
## GO:0044423 GO:0044423 virion component 0 0/39
## GO:0110165 GO:0110165 cellular anatomical entity 39 39/39
## geneID
## GO:0032991 RB1/HSPA1A/AKT1/MTOR/ETS1/ARID1A/MYH9/CDKN1A/FOXO3/ATM/CASP8/CCND1/PIK3R1/CHEK1/IGF1R/SRSF1/STAT5A/NCOA3/YAP1/ITGA2/TGM2/RBM15
## GO:0044423
## GO:0110165 RB1/XIAP/HSPA1A/AKT1/VHL/MTOR/MAPK8/ETS1/ARID1A/BID/MYH9/CDKN1A/FOXO3/ATM/CASP8/MACC1/PTEN/KRAS/NRAS/PTK2/CCND1/PIK3R1/CHEK1/IGF1R/SRSF1/TUBA1B/STAT5A/NCOA3/YAP1/ITGA2/MAPK1/GAB2/ANLN/TGM2/SQSTM1/G6PD/RBM15/FASN/TTF1
## ID Description Count GeneRatio
## GO:0003774 GO:0003774 cytoskeletal motor activity 1 1/44
## GO:0003824 GO:0003824 catalytic activity 24 24/44
## GO:0005198 GO:0005198 structural molecule activity 1 1/44
## GO:0005215 GO:0005215 transporter activity 2 2/44
## GO:0005488 GO:0005488 binding 44 44/44
## GO:0009055 GO:0009055 electron transfer activity 0 0/44
## geneID
## GO:0003774 MYH9
## GO:0003824 MET/G6PD/KRAS/CCND1/AKT1/IGF1R/HSPA1A/VHL/MTOR/MAPK8/CDKN1A/ATM/CASP8/PTEN/NRAS/PTK2/PARP1/RAB25/CASP3/CHEK1/MSH6/PIK3CA/MAPK1/TGM2
## GO:0005198 FN1
## GO:0005215 BCL2/IGF1R
## GO:0005488 ESR1/MET/G6PD/BCL2/KRAS/CCND1/NOTCH3/AKT1/IGF1R/HSPA1A/VHL/MTOR/MAPK8/MYH9/CDKN1A/FOXO3/ATM/CASP8/MACC1/PTEN/NRAS/PTK2/ETS1/PARP1/CCNE2/RAB25/YWHAZ/STAT5A/MYC/CASP3/BCL2L11/YAP1/CHEK1/FN1/MSH6/ITGA2/PIK3CA/MAPK1/SRSF1/ANLN/ERBB3/CDH2/CTNNB1/TGM2
## GO:0009055
## ID Description Count GeneRatio
## GO:0000003 GO:0000003 reproduction 18 18/44
## GO:0002376 GO:0002376 immune system process 26 26/44
## GO:0008152 GO:0008152 metabolic process 39 39/44
## GO:0009987 GO:0009987 cellular process 44 44/44
## GO:0016032 GO:0016032 viral process 4 4/44
## GO:0022414 GO:0022414 reproductive process 18 18/44
## geneID
## GO:0000003 ESR1/BCL2/AKT1/IGF1R/MTOR/MYH9/FOXO3/ATM/CASP8/PTEN/PARP1/CCNE2/CASP3/BCL2L11/MSH6/ITGA2/PIK3CA/CTNNB1
## GO:0002376 ESR1/G6PD/BCL2/AKT1/IGF1R/HSPA1A/MTOR/MAPK8/MYH9/CDKN1A/FOXO3/ATM/CASP8/PTK2/ETS1/PARP1/YWHAZ/MYC/CASP3/BCL2L11/FN1/MSH6/ITGA2/PIK3CA/MAPK1/CTNNB1
## GO:0008152 ESR1/MET/G6PD/BCL2/KRAS/CCND1/NOTCH3/AKT1/IGF1R/HSPA1A/VHL/MTOR/MAPK8/MYH9/CDKN1A/FOXO3/ATM/CASP8/MACC1/PTEN/PTK2/ETS1/PARP1/CCNE2/YWHAZ/STAT5A/MYC/CASP3/YAP1/CHEK1/FN1/MSH6/ITGA2/PIK3CA/MAPK1/SRSF1/ERBB3/CTNNB1/TGM2
## GO:0009987 ESR1/MET/G6PD/BCL2/KRAS/CCND1/NOTCH3/AKT1/IGF1R/HSPA1A/VHL/MTOR/MAPK8/MYH9/CDKN1A/FOXO3/ATM/CASP8/MACC1/PTEN/NRAS/PTK2/ETS1/PARP1/CCNE2/RAB25/YWHAZ/STAT5A/MYC/CASP3/BCL2L11/YAP1/CHEK1/FN1/MSH6/ITGA2/PIK3CA/MAPK1/SRSF1/ANLN/ERBB3/CDH2/CTNNB1/TGM2
## GO:0016032 BCL2/AKT1/HSPA1A/ITGA2
## GO:0022414 ESR1/BCL2/AKT1/IGF1R/MTOR/MYH9/FOXO3/ATM/CASP8/PTEN/PARP1/CCNE2/CASP3/BCL2L11/MSH6/ITGA2/PIK3CA/CTNNB1
## ID Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex 32 32/44
## GO:0044423 GO:0044423 virion component 0 0/44
## GO:0110165 GO:0110165 cellular anatomical entity 44 44/44
## geneID
## GO:0032991 ESR1/MET/BCL2/CCND1/NOTCH3/AKT1/IGF1R/HSPA1A/MTOR/MYH9/CDKN1A/FOXO3/ATM/CASP8/ETS1/PARP1/CCNE2/STAT5A/MYC/CASP3/BCL2L11/YAP1/CHEK1/FN1/MSH6/ITGA2/PIK3CA/SRSF1/ERBB3/CDH2/CTNNB1/TGM2
## GO:0044423
## GO:0110165 ESR1/MET/G6PD/BCL2/KRAS/CCND1/NOTCH3/AKT1/IGF1R/HSPA1A/VHL/MTOR/MAPK8/MYH9/CDKN1A/FOXO3/ATM/CASP8/MACC1/PTEN/NRAS/PTK2/ETS1/PARP1/CCNE2/RAB25/YWHAZ/STAT5A/MYC/CASP3/BCL2L11/YAP1/CHEK1/FN1/MSH6/ITGA2/PIK3CA/MAPK1/SRSF1/ANLN/ERBB3/CDH2/CTNNB1/TGM2
## ID Description Count GeneRatio
## GO:0003774 GO:0003774 cytoskeletal motor activity 1 1/26
## GO:0003824 GO:0003824 catalytic activity 15 15/26
## GO:0005198 GO:0005198 structural molecule activity 1 1/26
## GO:0005215 GO:0005215 transporter activity 1 1/26
## GO:0005488 GO:0005488 binding 26 26/26
## GO:0009055 GO:0009055 electron transfer activity 0 0/26
## geneID
## GO:0003774 MYH9
## GO:0003824 XIAP/MAPK8/CDKN1A/ATM/CASP8/CCND1/PIK3R1/CHEK1/IGF1R/TUBA1B/NCOA3/MAPK1/TGM2/G6PD/FASN
## GO:0005198 TUBA1B
## GO:0005215 IGF1R
## GO:0005488 ETS1/XIAP/MAPK8/ARID1A/BID/MYH9/CDKN1A/FOXO3/ATM/CASP8/MACC1/CCND1/PIK3R1/CHEK1/IGF1R/SRSF1/TUBA1B/STAT5A/NCOA3/GAB2/YAP1/MAPK1/ANLN/TGM2/G6PD/FASN
## GO:0009055
## ID Description Count GeneRatio
## GO:0000003 GO:0000003 reproduction 5 5/26
## GO:0002376 GO:0002376 immune system process 15 15/26
## GO:0008152 GO:0008152 metabolic process 23 23/26
## GO:0009987 GO:0009987 cellular process 26 26/26
## GO:0016032 GO:0016032 viral process 0 0/26
## GO:0022414 GO:0022414 reproductive process 5 5/26
## geneID
## GO:0000003 MYH9/FOXO3/ATM/CASP8/IGF1R
## GO:0002376 ETS1/XIAP/MAPK8/ARID1A/BID/MYH9/CDKN1A/FOXO3/ATM/CASP8/PIK3R1/IGF1R/GAB2/MAPK1/G6PD
## GO:0008152 ETS1/XIAP/MAPK8/ARID1A/BID/MYH9/CDKN1A/FOXO3/ATM/CASP8/MACC1/CCND1/PIK3R1/CHEK1/IGF1R/SRSF1/STAT5A/NCOA3/YAP1/MAPK1/TGM2/G6PD/FASN
## GO:0009987 ETS1/XIAP/MAPK8/ARID1A/BID/MYH9/CDKN1A/FOXO3/ATM/CASP8/MACC1/CCND1/PIK3R1/CHEK1/IGF1R/SRSF1/TUBA1B/STAT5A/NCOA3/GAB2/YAP1/MAPK1/ANLN/TGM2/G6PD/FASN
## GO:0016032
## GO:0022414 MYH9/FOXO3/ATM/CASP8/IGF1R
## ID Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex 16 16/26
## GO:0044423 GO:0044423 virion component 0 0/26
## GO:0110165 GO:0110165 cellular anatomical entity 26 26/26
## geneID
## GO:0032991 ETS1/ARID1A/MYH9/CDKN1A/FOXO3/ATM/CASP8/CCND1/PIK3R1/CHEK1/IGF1R/SRSF1/STAT5A/NCOA3/YAP1/TGM2
## GO:0044423
## GO:0110165 ETS1/XIAP/MAPK8/ARID1A/BID/MYH9/CDKN1A/FOXO3/ATM/CASP8/MACC1/CCND1/PIK3R1/CHEK1/IGF1R/SRSF1/TUBA1B/STAT5A/NCOA3/GAB2/YAP1/MAPK1/ANLN/TGM2/G6PD/FASN
## ID Description Count GeneRatio
## GO:0003774 GO:0003774 cytoskeletal motor activity 0 0/23
## GO:0003824 GO:0003824 catalytic activity 10 10/23
## GO:0005198 GO:0005198 structural molecule activity 1 1/23
## GO:0005215 GO:0005215 transporter activity 2 2/23
## GO:0005488 GO:0005488 binding 23 23/23
## GO:0009055 GO:0009055 electron transfer activity 0 0/23
## geneID
## GO:0003774
## GO:0003824 MET/G6PD/KRAS/CCND1/AKT1/IGF1R/XIAP/MAPK8/CHEK1/NCOA3
## GO:0005198 FN1
## GO:0005215 BCL2/IGF1R
## GO:0005488 ESR1/MET/G6PD/BCL2/KRAS/CCND1/NOTCH3/AKT1/IGF1R/ETS1/XIAP/MAPK8/ARID1A/BID/YWHAZ/FOXO3/CHEK1/FN1/NCOA3/GAB2/IGFBP2/CTNNB1/GATA3
## GO:0009055
## ID Description Count GeneRatio
## GO:0000003 GO:0000003 reproduction 8 8/23
## GO:0002376 GO:0002376 immune system process 17 17/23
## GO:0008152 GO:0008152 metabolic process 21 21/23
## GO:0009987 GO:0009987 cellular process 23 23/23
## GO:0016032 GO:0016032 viral process 2 2/23
## GO:0022414 GO:0022414 reproductive process 8 8/23
## geneID
## GO:0000003 ESR1/BCL2/AKT1/IGF1R/FOXO3/IGFBP2/CTNNB1/GATA3
## GO:0002376 ESR1/G6PD/BCL2/AKT1/IGF1R/ETS1/XIAP/MAPK8/ARID1A/BID/YWHAZ/FOXO3/FN1/GAB2/IGFBP2/CTNNB1/GATA3
## GO:0008152 ESR1/MET/G6PD/BCL2/KRAS/CCND1/NOTCH3/AKT1/IGF1R/ETS1/XIAP/MAPK8/ARID1A/BID/YWHAZ/FOXO3/CHEK1/FN1/NCOA3/CTNNB1/GATA3
## GO:0009987 ESR1/MET/G6PD/BCL2/KRAS/CCND1/NOTCH3/AKT1/IGF1R/ETS1/XIAP/MAPK8/ARID1A/BID/YWHAZ/FOXO3/CHEK1/FN1/NCOA3/GAB2/IGFBP2/CTNNB1/GATA3
## GO:0016032 BCL2/AKT1
## GO:0022414 ESR1/BCL2/AKT1/IGF1R/FOXO3/IGFBP2/CTNNB1/GATA3
## ID Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex 15 15/23
## GO:0044423 GO:0044423 virion component 0 0/23
## GO:0110165 GO:0110165 cellular anatomical entity 23 23/23
## geneID
## GO:0032991 ESR1/MET/BCL2/CCND1/NOTCH3/AKT1/IGF1R/ETS1/ARID1A/FOXO3/CHEK1/FN1/NCOA3/CTNNB1/GATA3
## GO:0044423
## GO:0110165 ESR1/MET/G6PD/BCL2/KRAS/CCND1/NOTCH3/AKT1/IGF1R/ETS1/XIAP/MAPK8/ARID1A/BID/YWHAZ/FOXO3/CHEK1/FN1/NCOA3/GAB2/IGFBP2/CTNNB1/GATA3
## ID Description Count GeneRatio
## GO:0003774 GO:0003774 cytoskeletal motor activity 1 1/40
## GO:0003824 GO:0003824 catalytic activity 23 23/40
## GO:0005198 GO:0005198 structural molecule activity 1 1/40
## GO:0005215 GO:0005215 transporter activity 1 1/40
## GO:0005488 GO:0005488 binding 40 40/40
## GO:0009055 GO:0009055 electron transfer activity 0 0/40
## geneID
## GO:0003774 MYH9
## GO:0003824 XIAP/HSPA1A/AKT1/VHL/MTOR/MAPK8/CDKN1A/ATM/CASP8/PTEN/KRAS/NRAS/PTK2/CCND1/PIK3R1/CHEK1/IGF1R/TUBA1B/NCOA3/MAPK1/TGM2/G6PD/FASN
## GO:0005198 TUBA1B
## GO:0005215 IGF1R
## GO:0005488 RB1/XIAP/HSPA1A/AKT1/VHL/MTOR/MAPK8/ETS1/ARID1A/BID/MYH9/CDKN1A/FOXO3/ATM/CASP8/MACC1/PTEN/KRAS/NRAS/PTK2/CCND1/PIK3R1/CHEK1/IGF1R/SRSF1/TUBA1B/STAT5A/NCOA3/YAP1/ITGA2/MAPK1/GAB2/ANLN/ERBB3/IGFBP2/TGM2/G6PD/FASN/TSC1/TTF1
## GO:0009055
## ID Description Count GeneRatio
## GO:0000003 GO:0000003 reproduction 11 11/40
## GO:0002376 GO:0002376 immune system process 23 23/40
## GO:0008152 GO:0008152 metabolic process 35 35/40
## GO:0009987 GO:0009987 cellular process 40 40/40
## GO:0016032 GO:0016032 viral process 3 3/40
## GO:0022414 GO:0022414 reproductive process 11 11/40
## geneID
## GO:0000003 RB1/AKT1/MTOR/MYH9/FOXO3/ATM/CASP8/PTEN/IGF1R/ITGA2/IGFBP2
## GO:0002376 RB1/XIAP/HSPA1A/AKT1/MTOR/MAPK8/ETS1/ARID1A/BID/MYH9/CDKN1A/FOXO3/ATM/CASP8/PTK2/PIK3R1/IGF1R/ITGA2/MAPK1/GAB2/IGFBP2/G6PD/TSC1
## GO:0008152 RB1/XIAP/HSPA1A/AKT1/VHL/MTOR/MAPK8/ETS1/ARID1A/BID/MYH9/CDKN1A/FOXO3/ATM/CASP8/MACC1/PTEN/KRAS/PTK2/CCND1/PIK3R1/CHEK1/IGF1R/SRSF1/STAT5A/NCOA3/YAP1/ITGA2/MAPK1/ERBB3/TGM2/G6PD/FASN/TSC1/TTF1
## GO:0009987 RB1/XIAP/HSPA1A/AKT1/VHL/MTOR/MAPK8/ETS1/ARID1A/BID/MYH9/CDKN1A/FOXO3/ATM/CASP8/MACC1/PTEN/KRAS/NRAS/PTK2/CCND1/PIK3R1/CHEK1/IGF1R/SRSF1/TUBA1B/STAT5A/NCOA3/YAP1/ITGA2/MAPK1/GAB2/ANLN/ERBB3/IGFBP2/TGM2/G6PD/FASN/TSC1/TTF1
## GO:0016032 HSPA1A/AKT1/ITGA2
## GO:0022414 RB1/AKT1/MTOR/MYH9/FOXO3/ATM/CASP8/PTEN/IGF1R/ITGA2/IGFBP2
## ID Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex 23 23/40
## GO:0044423 GO:0044423 virion component 0 0/40
## GO:0110165 GO:0110165 cellular anatomical entity 40 40/40
## geneID
## GO:0032991 RB1/HSPA1A/AKT1/MTOR/ETS1/ARID1A/MYH9/CDKN1A/FOXO3/ATM/CASP8/CCND1/PIK3R1/CHEK1/IGF1R/SRSF1/STAT5A/NCOA3/YAP1/ITGA2/ERBB3/TGM2/TSC1
## GO:0044423
## GO:0110165 RB1/XIAP/HSPA1A/AKT1/VHL/MTOR/MAPK8/ETS1/ARID1A/BID/MYH9/CDKN1A/FOXO3/ATM/CASP8/MACC1/PTEN/KRAS/NRAS/PTK2/CCND1/PIK3R1/CHEK1/IGF1R/SRSF1/TUBA1B/STAT5A/NCOA3/YAP1/ITGA2/MAPK1/GAB2/ANLN/ERBB3/IGFBP2/TGM2/G6PD/FASN/TSC1/TTF1
## ID Description Count GeneRatio
## GO:0003774 GO:0003774 cytoskeletal motor activity 1 1/41
## GO:0003824 GO:0003824 catalytic activity 26 26/41
## GO:0005198 GO:0005198 structural molecule activity 0 0/41
## GO:0005215 GO:0005215 transporter activity 2 2/41
## GO:0005488 GO:0005488 binding 41 41/41
## GO:0009055 GO:0009055 electron transfer activity 0 0/41
## geneID
## GO:0003774 MYH9
## GO:0003824 HSPA1A/AKT1/VHL/MTOR/MAPK8/CDKN1A/ATM/CASP8/PTEN/KRAS/NRAS/PTK2/PARP1/IGF1R/RAB25/CCND1/XIAP/CASP3/MSH6/PIK3CA/MAPK1/G6PD/TGM2/FASN/INPP4B/PRDX1
## GO:0005198
## GO:0005215 IGF1R/BCL2
## GO:0005488 HSPA1A/AKT1/VHL/MTOR/MAPK8/MYH9/CDKN1A/FOXO3/ATM/CASP8/MACC1/PTEN/KRAS/NRAS/PTK2/ETS1/PARP1/IGF1R/CCNE2/RAB25/CCND1/XIAP/STAT5A/BCL2/MYC/CASP3/BCL2L11/YAP1/MSH6/ITGA2/PIK3CA/MAPK1/SRSF1/ANLN/G6PD/TGM2/SQSTM1/FASN/INPP4B/TTF1/PRDX1
## GO:0009055
## ID Description Count GeneRatio
## GO:0000003 GO:0000003 reproduction 16 16/41
## GO:0002376 GO:0002376 immune system process 25 25/41
## GO:0008152 GO:0008152 metabolic process 37 37/41
## GO:0009987 GO:0009987 cellular process 41 41/41
## GO:0016032 GO:0016032 viral process 4 4/41
## GO:0022414 GO:0022414 reproductive process 16 16/41
## geneID
## GO:0000003 AKT1/MTOR/MYH9/FOXO3/ATM/CASP8/PTEN/PARP1/IGF1R/CCNE2/BCL2/CASP3/BCL2L11/MSH6/ITGA2/PIK3CA
## GO:0002376 HSPA1A/AKT1/MTOR/MAPK8/MYH9/CDKN1A/FOXO3/ATM/CASP8/PTK2/ETS1/PARP1/IGF1R/XIAP/BCL2/MYC/CASP3/BCL2L11/MSH6/ITGA2/PIK3CA/MAPK1/G6PD/SQSTM1/PRDX1
## GO:0008152 HSPA1A/AKT1/VHL/MTOR/MAPK8/MYH9/CDKN1A/FOXO3/ATM/CASP8/MACC1/PTEN/KRAS/PTK2/ETS1/PARP1/IGF1R/CCNE2/CCND1/XIAP/STAT5A/BCL2/MYC/CASP3/YAP1/MSH6/ITGA2/PIK3CA/MAPK1/SRSF1/G6PD/TGM2/SQSTM1/FASN/INPP4B/TTF1/PRDX1
## GO:0009987 HSPA1A/AKT1/VHL/MTOR/MAPK8/MYH9/CDKN1A/FOXO3/ATM/CASP8/MACC1/PTEN/KRAS/NRAS/PTK2/ETS1/PARP1/IGF1R/CCNE2/RAB25/CCND1/XIAP/STAT5A/BCL2/MYC/CASP3/BCL2L11/YAP1/MSH6/ITGA2/PIK3CA/MAPK1/SRSF1/ANLN/G6PD/TGM2/SQSTM1/FASN/INPP4B/TTF1/PRDX1
## GO:0016032 HSPA1A/AKT1/BCL2/ITGA2
## GO:0022414 AKT1/MTOR/MYH9/FOXO3/ATM/CASP8/PTEN/PARP1/IGF1R/CCNE2/BCL2/CASP3/BCL2L11/MSH6/ITGA2/PIK3CA
## ID Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex 24 24/41
## GO:0044423 GO:0044423 virion component 0 0/41
## GO:0110165 GO:0110165 cellular anatomical entity 41 41/41
## geneID
## GO:0032991 HSPA1A/AKT1/MTOR/MYH9/CDKN1A/FOXO3/ATM/CASP8/ETS1/PARP1/IGF1R/CCNE2/CCND1/STAT5A/BCL2/MYC/CASP3/BCL2L11/YAP1/MSH6/ITGA2/PIK3CA/SRSF1/TGM2
## GO:0044423
## GO:0110165 HSPA1A/AKT1/VHL/MTOR/MAPK8/MYH9/CDKN1A/FOXO3/ATM/CASP8/MACC1/PTEN/KRAS/NRAS/PTK2/ETS1/PARP1/IGF1R/CCNE2/RAB25/CCND1/XIAP/STAT5A/BCL2/MYC/CASP3/BCL2L11/YAP1/MSH6/ITGA2/PIK3CA/MAPK1/SRSF1/ANLN/G6PD/TGM2/SQSTM1/FASN/INPP4B/TTF1/PRDX1
## ID Description Count GeneRatio
## GO:0003774 GO:0003774 cytoskeletal motor activity 0 0/3
## GO:0003824 GO:0003824 catalytic activity 2 2/3
## GO:0005198 GO:0005198 structural molecule activity 0 0/3
## GO:0005215 GO:0005215 transporter activity 0 0/3
## GO:0005488 GO:0005488 binding 3 3/3
## GO:0009055 GO:0009055 electron transfer activity 0 0/3
## geneID
## GO:0003774
## GO:0003824 CDKN1A/TGM2
## GO:0005198
## GO:0005215
## GO:0005488 CDKN1A/STAT5A/TGM2
## GO:0009055
## ID Description Count GeneRatio geneID
## GO:0000003 GO:0000003 reproduction 0 0/3
## GO:0002376 GO:0002376 immune system process 1 1/3 CDKN1A
## GO:0008152 GO:0008152 metabolic process 3 3/3 CDKN1A/STAT5A/TGM2
## GO:0009987 GO:0009987 cellular process 3 3/3 CDKN1A/STAT5A/TGM2
## GO:0016032 GO:0016032 viral process 0 0/3
## GO:0022414 GO:0022414 reproductive process 0 0/3
## ID Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex 3 3/3
## GO:0044423 GO:0044423 virion component 0 0/3
## GO:0110165 GO:0110165 cellular anatomical entity 3 3/3
## geneID
## GO:0032991 CDKN1A/STAT5A/TGM2
## GO:0044423
## GO:0110165 CDKN1A/STAT5A/TGM2
## ID Description Count GeneRatio
## GO:0003774 GO:0003774 cytoskeletal motor activity 0 0/17
## GO:0003824 GO:0003824 catalytic activity 10 10/17
## GO:0005198 GO:0005198 structural molecule activity 1 1/17
## GO:0005215 GO:0005215 transporter activity 0 0/17
## GO:0005488 GO:0005488 binding 17 17/17
## GO:0009055 GO:0009055 electron transfer activity 0 0/17
## geneID
## GO:0003774
## GO:0003824 XIAP/MAPK8/PTEN/KRAS/NRAS/PTK2/ATM/NCOA3/CCND1/G6PD
## GO:0005198 FN1
## GO:0005215
## GO:0005488 ETS1/XIAP/MAPK8/ARID1A/BID/PTEN/KRAS/NRAS/PTK2/ATM/NCOA3/GAB2/ITGA2/IGFBP2/FN1/CCND1/G6PD
## GO:0009055
## ID Description Count GeneRatio
## GO:0000003 GO:0000003 reproduction 4 4/17
## GO:0002376 GO:0002376 immune system process 12 12/17
## GO:0008152 GO:0008152 metabolic process 14 14/17
## GO:0009987 GO:0009987 cellular process 17 17/17
## GO:0016032 GO:0016032 viral process 1 1/17
## GO:0022414 GO:0022414 reproductive process 4 4/17
## geneID
## GO:0000003 PTEN/ATM/ITGA2/IGFBP2
## GO:0002376 ETS1/XIAP/MAPK8/ARID1A/BID/PTK2/ATM/GAB2/ITGA2/IGFBP2/FN1/G6PD
## GO:0008152 ETS1/XIAP/MAPK8/ARID1A/BID/PTEN/KRAS/PTK2/ATM/NCOA3/ITGA2/FN1/CCND1/G6PD
## GO:0009987 ETS1/XIAP/MAPK8/ARID1A/BID/PTEN/KRAS/NRAS/PTK2/ATM/NCOA3/GAB2/ITGA2/IGFBP2/FN1/CCND1/G6PD
## GO:0016032 ITGA2
## GO:0022414 PTEN/ATM/ITGA2/IGFBP2
## ID Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex 7 7/17
## GO:0044423 GO:0044423 virion component 0 0/17
## GO:0110165 GO:0110165 cellular anatomical entity 17 17/17
## geneID
## GO:0032991 ETS1/ARID1A/ATM/NCOA3/ITGA2/FN1/CCND1
## GO:0044423
## GO:0110165 ETS1/XIAP/MAPK8/ARID1A/BID/PTEN/KRAS/NRAS/PTK2/ATM/NCOA3/GAB2/ITGA2/IGFBP2/FN1/CCND1/G6PD
## ID Description Count GeneRatio
## GO:0003774 GO:0003774 cytoskeletal motor activity 0 0/13
## GO:0003824 GO:0003824 catalytic activity 5 5/13
## GO:0005198 GO:0005198 structural molecule activity 1 1/13
## GO:0005215 GO:0005215 transporter activity 0 0/13
## GO:0005488 GO:0005488 binding 13 13/13
## GO:0009055 GO:0009055 electron transfer activity 0 0/13
## geneID
## GO:0003774
## GO:0003824 XIAP/MAPK8/NCOA3/CCND1/FASN
## GO:0005198 FN1
## GO:0005215
## GO:0005488 RB1/XIAP/ETS1/MAPK8/ARID1A/BID/YWHAZ/NCOA3/GAB2/FN1/CTNNB1/CCND1/FASN
## GO:0009055
## ID Description Count GeneRatio
## GO:0000003 GO:0000003 reproduction 2 2/13
## GO:0002376 GO:0002376 immune system process 10 10/13
## GO:0008152 GO:0008152 metabolic process 12 12/13
## GO:0009987 GO:0009987 cellular process 13 13/13
## GO:0016032 GO:0016032 viral process 0 0/13
## GO:0022414 GO:0022414 reproductive process 2 2/13
## geneID
## GO:0000003 RB1/CTNNB1
## GO:0002376 RB1/XIAP/ETS1/MAPK8/ARID1A/BID/YWHAZ/GAB2/FN1/CTNNB1
## GO:0008152 RB1/XIAP/ETS1/MAPK8/ARID1A/BID/YWHAZ/NCOA3/FN1/CTNNB1/CCND1/FASN
## GO:0009987 RB1/XIAP/ETS1/MAPK8/ARID1A/BID/YWHAZ/NCOA3/GAB2/FN1/CTNNB1/CCND1/FASN
## GO:0016032
## GO:0022414 RB1/CTNNB1
## ID Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex 7 7/13
## GO:0044423 GO:0044423 virion component 0 0/13
## GO:0110165 GO:0110165 cellular anatomical entity 13 13/13
## geneID
## GO:0032991 RB1/ETS1/ARID1A/NCOA3/FN1/CTNNB1/CCND1
## GO:0044423
## GO:0110165 RB1/XIAP/ETS1/MAPK8/ARID1A/BID/YWHAZ/NCOA3/GAB2/FN1/CTNNB1/CCND1/FASN
## ID Description Count GeneRatio
## GO:0003774 GO:0003774 cytoskeletal motor activity 1 1/25
## GO:0003824 GO:0003824 catalytic activity 16 16/25
## GO:0005198 GO:0005198 structural molecule activity 1 1/25
## GO:0005215 GO:0005215 transporter activity 0 0/25
## GO:0005488 GO:0005488 binding 25 25/25
## GO:0009055 GO:0009055 electron transfer activity 0 0/25
## geneID
## GO:0003774 MYH9
## GO:0003824 HSPA1A/AKT1/VHL/MTOR/MAPK8/CDKN1A/ATM/CASP8/PTEN/KRAS/NRAS/PTK2/CCND1/MAPK1/TGM2/G6PD
## GO:0005198 FN1
## GO:0005215
## GO:0005488 HSPA1A/AKT1/VHL/MTOR/MAPK8/MYH9/CDKN1A/FOXO3/ATM/CASP8/MACC1/PTEN/KRAS/NRAS/PTK2/ETS1/STAT5A/CCND1/YAP1/ITGA2/MAPK1/ANLN/FN1/TGM2/G6PD
## GO:0009055
## ID Description Count GeneRatio
## GO:0000003 GO:0000003 reproduction 8 8/25
## GO:0002376 GO:0002376 immune system process 15 15/25
## GO:0008152 GO:0008152 metabolic process 23 23/25
## GO:0009987 GO:0009987 cellular process 25 25/25
## GO:0016032 GO:0016032 viral process 3 3/25
## GO:0022414 GO:0022414 reproductive process 8 8/25
## geneID
## GO:0000003 AKT1/MTOR/MYH9/FOXO3/ATM/CASP8/PTEN/ITGA2
## GO:0002376 HSPA1A/AKT1/MTOR/MAPK8/MYH9/CDKN1A/FOXO3/ATM/CASP8/PTK2/ETS1/ITGA2/MAPK1/FN1/G6PD
## GO:0008152 HSPA1A/AKT1/VHL/MTOR/MAPK8/MYH9/CDKN1A/FOXO3/ATM/CASP8/MACC1/PTEN/KRAS/PTK2/ETS1/STAT5A/CCND1/YAP1/ITGA2/MAPK1/FN1/TGM2/G6PD
## GO:0009987 HSPA1A/AKT1/VHL/MTOR/MAPK8/MYH9/CDKN1A/FOXO3/ATM/CASP8/MACC1/PTEN/KRAS/NRAS/PTK2/ETS1/STAT5A/CCND1/YAP1/ITGA2/MAPK1/ANLN/FN1/TGM2/G6PD
## GO:0016032 HSPA1A/AKT1/ITGA2
## GO:0022414 AKT1/MTOR/MYH9/FOXO3/ATM/CASP8/PTEN/ITGA2
## ID Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex 15 15/25
## GO:0044423 GO:0044423 virion component 0 0/25
## GO:0110165 GO:0110165 cellular anatomical entity 25 25/25
## geneID
## GO:0032991 HSPA1A/AKT1/MTOR/MYH9/CDKN1A/FOXO3/ATM/CASP8/ETS1/STAT5A/CCND1/YAP1/ITGA2/FN1/TGM2
## GO:0044423
## GO:0110165 HSPA1A/AKT1/VHL/MTOR/MAPK8/MYH9/CDKN1A/FOXO3/ATM/CASP8/MACC1/PTEN/KRAS/NRAS/PTK2/ETS1/STAT5A/CCND1/YAP1/ITGA2/MAPK1/ANLN/FN1/TGM2/G6PD
## ID Description Count GeneRatio
## GO:0003774 GO:0003774 cytoskeletal motor activity 1 1/42
## GO:0003824 GO:0003824 catalytic activity 24 24/42
## GO:0005198 GO:0005198 structural molecule activity 1 1/42
## GO:0005215 GO:0005215 transporter activity 2 2/42
## GO:0005488 GO:0005488 binding 42 42/42
## GO:0009055 GO:0009055 electron transfer activity 0 0/42
## geneID
## GO:0003774 MYH9
## GO:0003824 MET/G6PD/KRAS/CCND1/AKT1/IGF1R/HSPA1A/VHL/MTOR/MAPK8/CDKN1A/ATM/CASP8/PTEN/NRAS/PTK2/PARP1/RAB25/CASP3/CHEK1/MSH6/PIK3CA/MAPK1/TGM2
## GO:0005198 FN1
## GO:0005215 BCL2/IGF1R
## GO:0005488 ESR1/MET/G6PD/BCL2/KRAS/CCND1/NOTCH3/AKT1/IGF1R/HSPA1A/VHL/MTOR/MAPK8/MYH9/CDKN1A/FOXO3/ATM/CASP8/MACC1/PTEN/NRAS/PTK2/ETS1/PARP1/CCNE2/RAB25/STAT5A/MYC/CASP3/BCL2L11/YAP1/CHEK1/FN1/MSH6/ITGA2/PIK3CA/MAPK1/SRSF1/ANLN/CTNNB1/TGM2/GATA3
## GO:0009055
## ID Description Count GeneRatio
## GO:0000003 GO:0000003 reproduction 19 19/42
## GO:0002376 GO:0002376 immune system process 26 26/42
## GO:0008152 GO:0008152 metabolic process 38 38/42
## GO:0009987 GO:0009987 cellular process 42 42/42
## GO:0016032 GO:0016032 viral process 4 4/42
## GO:0022414 GO:0022414 reproductive process 19 19/42
## geneID
## GO:0000003 ESR1/BCL2/AKT1/IGF1R/MTOR/MYH9/FOXO3/ATM/CASP8/PTEN/PARP1/CCNE2/CASP3/BCL2L11/MSH6/ITGA2/PIK3CA/CTNNB1/GATA3
## GO:0002376 ESR1/G6PD/BCL2/AKT1/IGF1R/HSPA1A/MTOR/MAPK8/MYH9/CDKN1A/FOXO3/ATM/CASP8/PTK2/ETS1/PARP1/MYC/CASP3/BCL2L11/FN1/MSH6/ITGA2/PIK3CA/MAPK1/CTNNB1/GATA3
## GO:0008152 ESR1/MET/G6PD/BCL2/KRAS/CCND1/NOTCH3/AKT1/IGF1R/HSPA1A/VHL/MTOR/MAPK8/MYH9/CDKN1A/FOXO3/ATM/CASP8/MACC1/PTEN/PTK2/ETS1/PARP1/CCNE2/STAT5A/MYC/CASP3/YAP1/CHEK1/FN1/MSH6/ITGA2/PIK3CA/MAPK1/SRSF1/CTNNB1/TGM2/GATA3
## GO:0009987 ESR1/MET/G6PD/BCL2/KRAS/CCND1/NOTCH3/AKT1/IGF1R/HSPA1A/VHL/MTOR/MAPK8/MYH9/CDKN1A/FOXO3/ATM/CASP8/MACC1/PTEN/NRAS/PTK2/ETS1/PARP1/CCNE2/RAB25/STAT5A/MYC/CASP3/BCL2L11/YAP1/CHEK1/FN1/MSH6/ITGA2/PIK3CA/MAPK1/SRSF1/ANLN/CTNNB1/TGM2/GATA3
## GO:0016032 BCL2/AKT1/HSPA1A/ITGA2
## GO:0022414 ESR1/BCL2/AKT1/IGF1R/MTOR/MYH9/FOXO3/ATM/CASP8/PTEN/PARP1/CCNE2/CASP3/BCL2L11/MSH6/ITGA2/PIK3CA/CTNNB1/GATA3
## ID Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex 31 31/42
## GO:0044423 GO:0044423 virion component 0 0/42
## GO:0110165 GO:0110165 cellular anatomical entity 42 42/42
## geneID
## GO:0032991 ESR1/MET/BCL2/CCND1/NOTCH3/AKT1/IGF1R/HSPA1A/MTOR/MYH9/CDKN1A/FOXO3/ATM/CASP8/ETS1/PARP1/CCNE2/STAT5A/MYC/CASP3/BCL2L11/YAP1/CHEK1/FN1/MSH6/ITGA2/PIK3CA/SRSF1/CTNNB1/TGM2/GATA3
## GO:0044423
## GO:0110165 ESR1/MET/G6PD/BCL2/KRAS/CCND1/NOTCH3/AKT1/IGF1R/HSPA1A/VHL/MTOR/MAPK8/MYH9/CDKN1A/FOXO3/ATM/CASP8/MACC1/PTEN/NRAS/PTK2/ETS1/PARP1/CCNE2/RAB25/STAT5A/MYC/CASP3/BCL2L11/YAP1/CHEK1/FN1/MSH6/ITGA2/PIK3CA/MAPK1/SRSF1/ANLN/CTNNB1/TGM2/GATA3
## ID Description Count GeneRatio
## GO:0003774 GO:0003774 cytoskeletal motor activity 0 0/8
## GO:0003824 GO:0003824 catalytic activity 4 4/8
## GO:0005198 GO:0005198 structural molecule activity 0 0/8
## GO:0005215 GO:0005215 transporter activity 0 0/8
## GO:0005488 GO:0005488 binding 8 8/8
## GO:0009055 GO:0009055 electron transfer activity 0 0/8
## geneID
## GO:0003774
## GO:0003824 XIAP/MAPK8/NCOA3/TGM2
## GO:0005198
## GO:0005215
## GO:0005488 ETS1/XIAP/MAPK8/ARID1A/BID/NCOA3/GAB2/TGM2
## GO:0009055
## ID Description Count GeneRatio
## GO:0000003 GO:0000003 reproduction 0 0/8
## GO:0002376 GO:0002376 immune system process 6 6/8
## GO:0008152 GO:0008152 metabolic process 7 7/8
## GO:0009987 GO:0009987 cellular process 8 8/8
## GO:0016032 GO:0016032 viral process 0 0/8
## GO:0022414 GO:0022414 reproductive process 0 0/8
## geneID
## GO:0000003
## GO:0002376 ETS1/XIAP/MAPK8/ARID1A/BID/GAB2
## GO:0008152 ETS1/XIAP/MAPK8/ARID1A/BID/NCOA3/TGM2
## GO:0009987 ETS1/XIAP/MAPK8/ARID1A/BID/NCOA3/GAB2/TGM2
## GO:0016032
## GO:0022414
## ID Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex 4 4/8
## GO:0044423 GO:0044423 virion component 0 0/8
## GO:0110165 GO:0110165 cellular anatomical entity 8 8/8
## geneID
## GO:0032991 ETS1/ARID1A/NCOA3/TGM2
## GO:0044423
## GO:0110165 ETS1/XIAP/MAPK8/ARID1A/BID/NCOA3/GAB2/TGM2
## ID Description Count GeneRatio geneID
## GO:0003774 GO:0003774 cytoskeletal motor activity 0 0/1
## GO:0003824 GO:0003824 catalytic activity 1 1/1 G6PD
## GO:0005198 GO:0005198 structural molecule activity 0 0/1
## GO:0005215 GO:0005215 transporter activity 0 0/1
## GO:0005488 GO:0005488 binding 1 1/1 G6PD
## GO:0009055 GO:0009055 electron transfer activity 0 0/1
## ID Description Count GeneRatio geneID
## GO:0000003 GO:0000003 reproduction 0 0/1
## GO:0002376 GO:0002376 immune system process 1 1/1 G6PD
## GO:0008152 GO:0008152 metabolic process 1 1/1 G6PD
## GO:0009987 GO:0009987 cellular process 1 1/1 G6PD
## GO:0016032 GO:0016032 viral process 0 0/1
## GO:0022414 GO:0022414 reproductive process 0 0/1
## ID Description Count GeneRatio geneID
## GO:0032991 GO:0032991 protein-containing complex 0 0/1
## GO:0044423 GO:0044423 virion component 0 0/1
## GO:0110165 GO:0110165 cellular anatomical entity 1 1/1 G6PD
## ID Description Count GeneRatio geneID
## GO:0003774 GO:0003774 cytoskeletal motor activity 0 0/0
## GO:0003824 GO:0003824 catalytic activity 0 0/0
## GO:0005198 GO:0005198 structural molecule activity 0 0/0
## GO:0005215 GO:0005215 transporter activity 0 0/0
## GO:0005488 GO:0005488 binding 0 0/0
## GO:0009055 GO:0009055 electron transfer activity 0 0/0
## ID Description Count GeneRatio geneID
## GO:0000003 GO:0000003 reproduction 0 0/0
## GO:0002376 GO:0002376 immune system process 0 0/0
## GO:0008152 GO:0008152 metabolic process 0 0/0
## GO:0009987 GO:0009987 cellular process 0 0/0
## GO:0016032 GO:0016032 viral process 0 0/0
## GO:0022414 GO:0022414 reproductive process 0 0/0
## ID Description Count GeneRatio geneID
## GO:0032991 GO:0032991 protein-containing complex 0 0/0
## GO:0044423 GO:0044423 virion component 0 0/0
## GO:0110165 GO:0110165 cellular anatomical entity 0 0/0
## ID Description Count GeneRatio
## GO:0003774 GO:0003774 cytoskeletal motor activity 0 0/8
## GO:0003824 GO:0003824 catalytic activity 7 7/8
## GO:0005198 GO:0005198 structural molecule activity 1 1/8
## GO:0005215 GO:0005215 transporter activity 1 1/8
## GO:0005488 GO:0005488 binding 8 8/8
## GO:0009055 GO:0009055 electron transfer activity 0 0/8
## geneID
## GO:0003774
## GO:0003824 CCND1/PIK3R1/XIAP/CHEK1/IGF1R/TUBA1B/FASN
## GO:0005198 TUBA1B
## GO:0005215 IGF1R
## GO:0005488 CCND1/PIK3R1/XIAP/CHEK1/IGF1R/SRSF1/TUBA1B/FASN
## GO:0009055
## ID Description Count GeneRatio
## GO:0000003 GO:0000003 reproduction 1 1/8
## GO:0002376 GO:0002376 immune system process 3 3/8
## GO:0008152 GO:0008152 metabolic process 7 7/8
## GO:0009987 GO:0009987 cellular process 8 8/8
## GO:0016032 GO:0016032 viral process 0 0/8
## GO:0022414 GO:0022414 reproductive process 1 1/8
## geneID
## GO:0000003 IGF1R
## GO:0002376 PIK3R1/XIAP/IGF1R
## GO:0008152 CCND1/PIK3R1/XIAP/CHEK1/IGF1R/SRSF1/FASN
## GO:0009987 CCND1/PIK3R1/XIAP/CHEK1/IGF1R/SRSF1/TUBA1B/FASN
## GO:0016032
## GO:0022414 IGF1R
## ID Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex 5 5/8
## GO:0044423 GO:0044423 virion component 0 0/8
## GO:0110165 GO:0110165 cellular anatomical entity 8 8/8
## geneID
## GO:0032991 CCND1/PIK3R1/CHEK1/IGF1R/SRSF1
## GO:0044423
## GO:0110165 CCND1/PIK3R1/XIAP/CHEK1/IGF1R/SRSF1/TUBA1B/FASN
## ID Description Count GeneRatio
## GO:0003774 GO:0003774 cytoskeletal motor activity 0 0/57
## GO:0003824 GO:0003824 catalytic activity 25 25/57
## GO:0005198 GO:0005198 structural molecule activity 1 1/57
## GO:0005215 GO:0005215 transporter activity 2 2/57
## GO:0005488 GO:0005488 binding 57 57/57
## GO:0009055 GO:0009055 electron transfer activity 0 0/57
## geneID
## GO:0003774
## GO:0003824 MET/BAP1/G6PD/KRAS/CCND1/AKT1/IGF1R/PTEN/EZH2/XIAP/MAPK8/NRAS/PTK2/ATM/CHEK2/NCOA3/AXL/CDKN1A/EGFR/CASP3/ASNS/CHEK1/RET/INPP4B/RAD50
## GO:0005198 FN1
## GO:0005215 BCL2/IGF1R
## GO:0005488 ESR1/MET/BAP1/ERRFI1/G6PD/BCL2/KRAS/CCND1/NOTCH3/AKT1/IGF1R/PTEN/CDKN1B/IRS1/MYC/JUN/BCL2L11/EZH2/SHC1/XIAP/ETS1/MAPK8/ARID1A/BID/NRAS/PTK2/ATM/YWHAZ/MAPT/CHEK2/NCOA3/AXL/CDKN1A/EGFR/CAV1/CASP3/ANXA1/TFF1/FOXO3/STAT3/ASNS/CHEK1/FOXM1/FN1/IGFBP2/ITGA2/RET/SQSTM1/CCNE2/GAB2/NDRG1/INPP4B/LCN2/RAD50/GATA3/CTNNB1/RBM15
## GO:0009055
## ID Description Count GeneRatio
## GO:0000003 GO:0000003 reproduction 20 20/57
## GO:0002376 GO:0002376 immune system process 36 36/57
## GO:0008152 GO:0008152 metabolic process 52 52/57
## GO:0009987 GO:0009987 cellular process 57 57/57
## GO:0016032 GO:0016032 viral process 7 7/57
## GO:0022414 GO:0022414 reproductive process 19 19/57
## geneID
## GO:0000003 ESR1/ERRFI1/BCL2/AKT1/IGF1R/PTEN/CDKN1B/BCL2L11/ATM/AXL/EGFR/CASP3/FOXO3/STAT3/IGFBP2/ITGA2/CCNE2/RAD50/GATA3/CTNNB1
## GO:0002376 ESR1/BAP1/G6PD/BCL2/AKT1/IGF1R/MYC/BCL2L11/EZH2/XIAP/ETS1/MAPK8/ARID1A/BID/PTK2/ATM/YWHAZ/MAPT/AXL/CDKN1A/CAV1/CASP3/ANXA1/FOXO3/STAT3/FN1/IGFBP2/ITGA2/RET/SQSTM1/GAB2/NDRG1/LCN2/GATA3/CTNNB1/RBM15
## GO:0008152 ESR1/MET/BAP1/ERRFI1/G6PD/BCL2/KRAS/CCND1/NOTCH3/AKT1/IGF1R/PTEN/CDKN1B/IRS1/MYC/JUN/EZH2/SHC1/XIAP/ETS1/MAPK8/ARID1A/BID/PTK2/ATM/YWHAZ/MAPT/CHEK2/NCOA3/AXL/CDKN1A/EGFR/CAV1/CASP3/ANXA1/TFF1/FOXO3/STAT3/ASNS/CHEK1/FOXM1/FN1/ITGA2/RET/SQSTM1/CCNE2/INPP4B/LCN2/RAD50/GATA3/CTNNB1/RBM15
## GO:0009987 ESR1/MET/BAP1/ERRFI1/G6PD/BCL2/KRAS/CCND1/NOTCH3/AKT1/IGF1R/PTEN/CDKN1B/IRS1/MYC/JUN/BCL2L11/EZH2/SHC1/XIAP/ETS1/MAPK8/ARID1A/BID/NRAS/PTK2/ATM/YWHAZ/MAPT/CHEK2/NCOA3/AXL/CDKN1A/EGFR/CAV1/CASP3/ANXA1/TFF1/FOXO3/STAT3/ASNS/CHEK1/FOXM1/FN1/IGFBP2/ITGA2/RET/SQSTM1/CCNE2/GAB2/NDRG1/INPP4B/LCN2/RAD50/GATA3/CTNNB1/RBM15
## GO:0016032 BCL2/AKT1/JUN/AXL/EGFR/CAV1/ITGA2
## GO:0022414 ESR1/ERRFI1/BCL2/AKT1/IGF1R/PTEN/CDKN1B/BCL2L11/ATM/AXL/EGFR/CASP3/FOXO3/IGFBP2/ITGA2/CCNE2/RAD50/GATA3/CTNNB1
## ID Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex 37 37/57
## GO:0044423 GO:0044423 virion component 0 0/57
## GO:0110165 GO:0110165 cellular anatomical entity 57 57/57
## geneID
## GO:0032991 ESR1/MET/BAP1/BCL2/CCND1/NOTCH3/AKT1/IGF1R/CDKN1B/IRS1/MYC/JUN/BCL2L11/EZH2/SHC1/ETS1/ARID1A/ATM/MAPT/NCOA3/AXL/CDKN1A/EGFR/CAV1/CASP3/FOXO3/STAT3/CHEK1/FOXM1/FN1/ITGA2/RET/CCNE2/RAD50/GATA3/CTNNB1/RBM15
## GO:0044423
## GO:0110165 ESR1/MET/BAP1/ERRFI1/G6PD/BCL2/KRAS/CCND1/NOTCH3/AKT1/IGF1R/PTEN/CDKN1B/IRS1/MYC/JUN/BCL2L11/EZH2/SHC1/XIAP/ETS1/MAPK8/ARID1A/BID/NRAS/PTK2/ATM/YWHAZ/MAPT/CHEK2/NCOA3/AXL/CDKN1A/EGFR/CAV1/CASP3/ANXA1/TFF1/FOXO3/STAT3/ASNS/CHEK1/FOXM1/FN1/IGFBP2/ITGA2/RET/SQSTM1/CCNE2/GAB2/NDRG1/INPP4B/LCN2/RAD50/GATA3/CTNNB1/RBM15
## ID Description Count GeneRatio
## GO:0003774 GO:0003774 cytoskeletal motor activity 1 1/32
## GO:0003824 GO:0003824 catalytic activity 19 19/32
## GO:0005198 GO:0005198 structural molecule activity 1 1/32
## GO:0005215 GO:0005215 transporter activity 2 2/32
## GO:0005488 GO:0005488 binding 32 32/32
## GO:0009055 GO:0009055 electron transfer activity 0 0/32
## geneID
## GO:0003774 MYH9
## GO:0003824 MET/G6PD/KRAS/CCND1/AKT1/IGF1R/HSPA1A/VHL/MTOR/MAPK8/CDKN1A/ATM/CASP8/PTEN/NRAS/PTK2/CHEK1/MAPK1/TGM2
## GO:0005198 FN1
## GO:0005215 BCL2/IGF1R
## GO:0005488 ESR1/MET/G6PD/BCL2/KRAS/CCND1/NOTCH3/AKT1/IGF1R/HSPA1A/VHL/MTOR/MAPK8/MYH9/CDKN1A/FOXO3/ATM/CASP8/MACC1/PTEN/NRAS/PTK2/ETS1/STAT5A/YAP1/CHEK1/FN1/ITGA2/MAPK1/ANLN/ERBB3/TGM2
## GO:0009055
## ID Description Count GeneRatio
## GO:0000003 GO:0000003 reproduction 11 11/32
## GO:0002376 GO:0002376 immune system process 18 18/32
## GO:0008152 GO:0008152 metabolic process 30 30/32
## GO:0009987 GO:0009987 cellular process 32 32/32
## GO:0016032 GO:0016032 viral process 4 4/32
## GO:0022414 GO:0022414 reproductive process 11 11/32
## geneID
## GO:0000003 ESR1/BCL2/AKT1/IGF1R/MTOR/MYH9/FOXO3/ATM/CASP8/PTEN/ITGA2
## GO:0002376 ESR1/G6PD/BCL2/AKT1/IGF1R/HSPA1A/MTOR/MAPK8/MYH9/CDKN1A/FOXO3/ATM/CASP8/PTK2/ETS1/FN1/ITGA2/MAPK1
## GO:0008152 ESR1/MET/G6PD/BCL2/KRAS/CCND1/NOTCH3/AKT1/IGF1R/HSPA1A/VHL/MTOR/MAPK8/MYH9/CDKN1A/FOXO3/ATM/CASP8/MACC1/PTEN/PTK2/ETS1/STAT5A/YAP1/CHEK1/FN1/ITGA2/MAPK1/ERBB3/TGM2
## GO:0009987 ESR1/MET/G6PD/BCL2/KRAS/CCND1/NOTCH3/AKT1/IGF1R/HSPA1A/VHL/MTOR/MAPK8/MYH9/CDKN1A/FOXO3/ATM/CASP8/MACC1/PTEN/NRAS/PTK2/ETS1/STAT5A/YAP1/CHEK1/FN1/ITGA2/MAPK1/ANLN/ERBB3/TGM2
## GO:0016032 BCL2/AKT1/HSPA1A/ITGA2
## GO:0022414 ESR1/BCL2/AKT1/IGF1R/MTOR/MYH9/FOXO3/ATM/CASP8/PTEN/ITGA2
## ID Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex 22 22/32
## GO:0044423 GO:0044423 virion component 0 0/32
## GO:0110165 GO:0110165 cellular anatomical entity 32 32/32
## geneID
## GO:0032991 ESR1/MET/BCL2/CCND1/NOTCH3/AKT1/IGF1R/HSPA1A/MTOR/MYH9/CDKN1A/FOXO3/ATM/CASP8/ETS1/STAT5A/YAP1/CHEK1/FN1/ITGA2/ERBB3/TGM2
## GO:0044423
## GO:0110165 ESR1/MET/G6PD/BCL2/KRAS/CCND1/NOTCH3/AKT1/IGF1R/HSPA1A/VHL/MTOR/MAPK8/MYH9/CDKN1A/FOXO3/ATM/CASP8/MACC1/PTEN/NRAS/PTK2/ETS1/STAT5A/YAP1/CHEK1/FN1/ITGA2/MAPK1/ANLN/ERBB3/TGM2
## ID Description Count GeneRatio
## GO:0003774 GO:0003774 cytoskeletal motor activity 1 1/53
## GO:0003824 GO:0003824 catalytic activity 32 32/53
## GO:0005198 GO:0005198 structural molecule activity 1 1/53
## GO:0005215 GO:0005215 transporter activity 2 2/53
## GO:0005488 GO:0005488 binding 53 53/53
## GO:0009055 GO:0009055 electron transfer activity 0 0/53
## geneID
## GO:0003774 MYH9
## GO:0003824 XIAP/HSPA1A/AKT1/VHL/MTOR/MAPK8/CDKN1A/ATM/CASP8/PTEN/KRAS/NRAS/PTK2/PARP1/IGF1R/RAB25/CCND1/PIK3R1/CHEK1/TUBA1B/NCOA3/CASP3/MSH6/PIK3CA/MAPK1/G6PD/MET/FASN/TGM2/BRCA2/INPP4B/PRDX1
## GO:0005198 TUBA1B
## GO:0005215 IGF1R/BCL2
## GO:0005488 RB1/XIAP/HSPA1A/AKT1/VHL/MTOR/MAPK8/ETS1/ARID1A/BID/MYH9/CDKN1A/FOXO3/ATM/CASP8/MACC1/PTEN/KRAS/NRAS/PTK2/PARP1/IGF1R/CCNE2/RAB25/CCND1/PIK3R1/CHEK1/SRSF1/TUBA1B/STAT5A/CDKN1B/BCL2L11/BCL2/NCOA3/MYC/CASP3/YAP1/MSH6/ITGA2/PIK3CA/MAPK1/GAB2/ANLN/G6PD/MET/FASN/TGM2/PXN/SQSTM1/BRCA2/INPP4B/TTF1/PRDX1
## GO:0009055
## ID Description Count GeneRatio
## GO:0000003 GO:0000003 reproduction 19 19/53
## GO:0002376 GO:0002376 immune system process 30 30/53
## GO:0008152 GO:0008152 metabolic process 46 46/53
## GO:0009987 GO:0009987 cellular process 53 53/53
## GO:0016032 GO:0016032 viral process 4 4/53
## GO:0022414 GO:0022414 reproductive process 19 19/53
## geneID
## GO:0000003 RB1/AKT1/MTOR/MYH9/FOXO3/ATM/CASP8/PTEN/PARP1/IGF1R/CCNE2/CDKN1B/BCL2L11/BCL2/CASP3/MSH6/ITGA2/PIK3CA/BRCA2
## GO:0002376 RB1/XIAP/HSPA1A/AKT1/MTOR/MAPK8/ETS1/ARID1A/BID/MYH9/CDKN1A/FOXO3/ATM/CASP8/PTK2/PARP1/IGF1R/PIK3R1/BCL2L11/BCL2/MYC/CASP3/MSH6/ITGA2/PIK3CA/MAPK1/GAB2/G6PD/SQSTM1/PRDX1
## GO:0008152 RB1/XIAP/HSPA1A/AKT1/VHL/MTOR/MAPK8/ETS1/ARID1A/BID/MYH9/CDKN1A/FOXO3/ATM/CASP8/MACC1/PTEN/KRAS/PTK2/PARP1/IGF1R/CCNE2/CCND1/PIK3R1/CHEK1/SRSF1/STAT5A/CDKN1B/BCL2/NCOA3/MYC/CASP3/YAP1/MSH6/ITGA2/PIK3CA/MAPK1/G6PD/MET/FASN/TGM2/SQSTM1/BRCA2/INPP4B/TTF1/PRDX1
## GO:0009987 RB1/XIAP/HSPA1A/AKT1/VHL/MTOR/MAPK8/ETS1/ARID1A/BID/MYH9/CDKN1A/FOXO3/ATM/CASP8/MACC1/PTEN/KRAS/NRAS/PTK2/PARP1/IGF1R/CCNE2/RAB25/CCND1/PIK3R1/CHEK1/SRSF1/TUBA1B/STAT5A/CDKN1B/BCL2L11/BCL2/NCOA3/MYC/CASP3/YAP1/MSH6/ITGA2/PIK3CA/MAPK1/GAB2/ANLN/G6PD/MET/FASN/TGM2/PXN/SQSTM1/BRCA2/INPP4B/TTF1/PRDX1
## GO:0016032 HSPA1A/AKT1/BCL2/ITGA2
## GO:0022414 RB1/AKT1/MTOR/MYH9/FOXO3/ATM/CASP8/PTEN/PARP1/IGF1R/CCNE2/CDKN1B/BCL2L11/BCL2/CASP3/MSH6/ITGA2/PIK3CA/BRCA2
## ID Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex 33 33/53
## GO:0044423 GO:0044423 virion component 0 0/53
## GO:0110165 GO:0110165 cellular anatomical entity 53 53/53
## geneID
## GO:0032991 RB1/HSPA1A/AKT1/MTOR/ETS1/ARID1A/MYH9/CDKN1A/FOXO3/ATM/CASP8/PARP1/IGF1R/CCNE2/CCND1/PIK3R1/CHEK1/SRSF1/STAT5A/CDKN1B/BCL2L11/BCL2/NCOA3/MYC/CASP3/YAP1/MSH6/ITGA2/PIK3CA/MET/TGM2/PXN/BRCA2
## GO:0044423
## GO:0110165 RB1/XIAP/HSPA1A/AKT1/VHL/MTOR/MAPK8/ETS1/ARID1A/BID/MYH9/CDKN1A/FOXO3/ATM/CASP8/MACC1/PTEN/KRAS/NRAS/PTK2/PARP1/IGF1R/CCNE2/RAB25/CCND1/PIK3R1/CHEK1/SRSF1/TUBA1B/STAT5A/CDKN1B/BCL2L11/BCL2/NCOA3/MYC/CASP3/YAP1/MSH6/ITGA2/PIK3CA/MAPK1/GAB2/ANLN/G6PD/MET/FASN/TGM2/PXN/SQSTM1/BRCA2/INPP4B/TTF1/PRDX1
## ID Description Count GeneRatio
## GO:0003774 GO:0003774 cytoskeletal motor activity 1 1/58
## GO:0003824 GO:0003824 catalytic activity 28 28/58
## GO:0005198 GO:0005198 structural molecule activity 1 1/58
## GO:0005215 GO:0005215 transporter activity 1 1/58
## GO:0005488 GO:0005488 binding 58 58/58
## GO:0009055 GO:0009055 electron transfer activity 0 0/58
## geneID
## GO:0003774 MYH9
## GO:0003824 XIAP/HSPA1A/AKT1/VHL/MTOR/MAPK8/CDKN1A/ATM/CASP8/CCND1/PIK3R1/CHEK1/IGF1R/TUBA1B/NRAS/PTEN/NCOA3/CASP9/CCNE1/MAPK9/RAF1/AKT2/PRKCA/MAPK1/MAPK3/FASN/TGM2/G6PD
## GO:0005198 TUBA1B
## GO:0005215 IGF1R
## GO:0005488 RB1/XIAP/HSPA1A/AKT1/VHL/MTOR/MAPK8/ETS1/ARID1A/BID/MYH9/CDKN1A/FOXO3/ATM/CASP8/MACC1/YWHAZ/CCND1/PIK3R1/CHEK1/IGF1R/SRSF1/TUBA1B/NRAS/STAT5A/PTEN/NCOA3/E2F1/CASP9/CDKN2A/CCNE1/MAPK9/RAF1/AKT2/YAP1/BCL2L1/DVL3/SMAD3/PRKCA/MAPK1/MAPK3/GAB2/ANLN/AKT1S1/IGFBP2/GATA3/FASN/CTNNB1/TGM2/PXN/RPTOR/SQSTM1/G6PD/RBM15/TSC1/TTF1/AR/TFRC
## GO:0009055
## ID Description Count GeneRatio
## GO:0000003 GO:0000003 reproduction 15 15/58
## GO:0002376 GO:0002376 immune system process 33 33/58
## GO:0008152 GO:0008152 metabolic process 51 51/58
## GO:0009987 GO:0009987 cellular process 58 58/58
## GO:0016032 GO:0016032 viral process 3 3/58
## GO:0022414 GO:0022414 reproductive process 15 15/58
## geneID
## GO:0000003 RB1/AKT1/MTOR/MYH9/FOXO3/ATM/CASP8/IGF1R/PTEN/CCNE1/BCL2L1/IGFBP2/GATA3/CTNNB1/AR
## GO:0002376 RB1/XIAP/HSPA1A/AKT1/MTOR/MAPK8/ETS1/ARID1A/BID/MYH9/CDKN1A/FOXO3/ATM/CASP8/YWHAZ/PIK3R1/IGF1R/MAPK9/RAF1/SMAD3/PRKCA/MAPK1/MAPK3/GAB2/IGFBP2/GATA3/CTNNB1/RPTOR/SQSTM1/G6PD/RBM15/TSC1/TFRC
## GO:0008152 RB1/XIAP/HSPA1A/AKT1/VHL/MTOR/MAPK8/ETS1/ARID1A/BID/MYH9/CDKN1A/FOXO3/ATM/CASP8/MACC1/YWHAZ/CCND1/PIK3R1/CHEK1/IGF1R/SRSF1/STAT5A/PTEN/NCOA3/E2F1/CASP9/CDKN2A/CCNE1/MAPK9/RAF1/AKT2/YAP1/DVL3/SMAD3/PRKCA/MAPK1/MAPK3/AKT1S1/GATA3/FASN/CTNNB1/TGM2/RPTOR/SQSTM1/G6PD/RBM15/TSC1/TTF1/AR/TFRC
## GO:0009987 RB1/XIAP/HSPA1A/AKT1/VHL/MTOR/MAPK8/ETS1/ARID1A/BID/MYH9/CDKN1A/FOXO3/ATM/CASP8/MACC1/YWHAZ/CCND1/PIK3R1/CHEK1/IGF1R/SRSF1/TUBA1B/NRAS/STAT5A/PTEN/NCOA3/E2F1/CASP9/CDKN2A/CCNE1/MAPK9/RAF1/AKT2/YAP1/BCL2L1/DVL3/SMAD3/PRKCA/MAPK1/MAPK3/GAB2/ANLN/AKT1S1/IGFBP2/GATA3/FASN/CTNNB1/TGM2/PXN/RPTOR/SQSTM1/G6PD/RBM15/TSC1/TTF1/AR/TFRC
## GO:0016032 HSPA1A/AKT1/TFRC
## GO:0022414 RB1/AKT1/MTOR/MYH9/FOXO3/ATM/CASP8/IGF1R/PTEN/CCNE1/BCL2L1/IGFBP2/GATA3/CTNNB1/AR
## ID Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex 37 37/58
## GO:0044423 GO:0044423 virion component 0 0/58
## GO:0110165 GO:0110165 cellular anatomical entity 58 58/58
## geneID
## GO:0032991 RB1/HSPA1A/AKT1/MTOR/ETS1/ARID1A/MYH9/CDKN1A/FOXO3/ATM/CASP8/CCND1/PIK3R1/CHEK1/IGF1R/SRSF1/STAT5A/NCOA3/E2F1/CASP9/CDKN2A/CCNE1/YAP1/BCL2L1/DVL3/SMAD3/PRKCA/AKT1S1/GATA3/CTNNB1/TGM2/PXN/RPTOR/RBM15/TSC1/AR/TFRC
## GO:0044423
## GO:0110165 RB1/XIAP/HSPA1A/AKT1/VHL/MTOR/MAPK8/ETS1/ARID1A/BID/MYH9/CDKN1A/FOXO3/ATM/CASP8/MACC1/YWHAZ/CCND1/PIK3R1/CHEK1/IGF1R/SRSF1/TUBA1B/NRAS/STAT5A/PTEN/NCOA3/E2F1/CASP9/CDKN2A/CCNE1/MAPK9/RAF1/AKT2/YAP1/BCL2L1/DVL3/SMAD3/PRKCA/MAPK1/MAPK3/GAB2/ANLN/AKT1S1/IGFBP2/GATA3/FASN/CTNNB1/TGM2/PXN/RPTOR/SQSTM1/G6PD/RBM15/TSC1/TTF1/AR/TFRCbarplot(ggo_MF[[1]], title = "groupGO, Molecular Function, Bicluster 1 of 1")
barplot(ggo_MF[[2]], title = "groupGO, Molecular Function, Bicluster 1 of 2")
barplot(ggo_MF[[3]], title = "groupGO, Molecular Function, Bicluster 2 of 2")
barplot(ggo_MF[[4]], title = "groupGO, Molecular Function, Bicluster 1 of 3")
barplot(ggo_MF[[5]], title = "groupGO, Molecular Function, Bicluster 2 of 3")
barplot(ggo_MF[[6]], title = "groupGO, Molecular Function, Bicluster 3 of 3")
barplot(ggo_MF[[7]], title = "groupGO, Molecular Function, Bicluster 1 of 5")
barplot(ggo_MF[[8]], title = "groupGO, Molecular Function, Bicluster 2 of 5")
barplot(ggo_MF[[9]], title = "groupGO, Molecular Function, Bicluster 3 of 5")
barplot(ggo_MF[[10]], title = "groupGO, Molecular Function, Bicluster 4 of 5")
barplot(ggo_MF[[11]], title = "groupGO, Molecular Function, Bicluster 5 of 5")
barplot(ggo_MF[[12]], title = "groupGO, Molecular Function, Bicluster 1 of 10")
barplot(ggo_MF[[13]], title = "groupGO, Molecular Function, Bicluster 2 of 10")
barplot(ggo_MF[[14]], title = "groupGO, Molecular Function, Bicluster 3 of 10")
barplot(ggo_MF[[15]], title = "groupGO, Molecular Function, Bicluster 4 of 10")
barplot(ggo_MF[[16]], title = "groupGO, Molecular Function, Bicluster 5 of 10")
barplot(ggo_MF[[17]], title = "groupGO, Molecular Function, Bicluster 6 of 10")
barplot(ggo_MF[[18]], title = "groupGO, Molecular Function, Bicluster 7 of 10")
barplot(ggo_MF[[19]], title = "groupGO, Molecular Function, Bicluster 8 of 10")
barplot(ggo_MF[[20]], title = "groupGO, Molecular Function, Bicluster 9 of 10")
barplot(ggo_MF[[21]], title = "groupGO, Molecular Function, Bicluster 10 of 10")
barplot(ggo_BP[[1]], title = "groupGO, Biological Process, Bicluster 1 of 1")
barplot(ggo_BP[[2]], title = "groupGO, Biological Process, Bicluster 1 of 2")
barplot(ggo_BP[[3]], title = "groupGO, Biological Process, Bicluster 2 of 2")
barplot(ggo_BP[[4]], title = "groupGO, Biological Process, Bicluster 1 of 3")
barplot(ggo_BP[[5]], title = "groupGO, Biological Process, Bicluster 2 of 3")
barplot(ggo_BP[[6]], title = "groupGO, Biological Process, Bicluster 3 of 3")
barplot(ggo_BP[[7]], title = "groupGO, Biological Process, Bicluster 1 of 5")
barplot(ggo_BP[[8]], title = "groupGO, Biological Process, Bicluster 2 of 5")
barplot(ggo_BP[[9]], title = "groupGO, Biological Process, Bicluster 3 of 5")
barplot(ggo_BP[[10]], title = "groupGO, Biological Process, Bicluster 4 of 5")
barplot(ggo_BP[[11]], title = "groupGO, Biological Process, Bicluster 5 of 5")
barplot(ggo_BP[[12]], title = "groupGO, Biological Process, Bicluster 1 of 10")
barplot(ggo_BP[[13]], title = "groupGO, Biological Process, Bicluster 2 of 10")
barplot(ggo_BP[[14]], title = "groupGO, Biological Process, Bicluster 3 of 10")
barplot(ggo_BP[[15]], title = "groupGO, Biological Process, Bicluster 4 of 10")
barplot(ggo_BP[[16]], title = "groupGO, Biological Process, Bicluster 5 of 10")
barplot(ggo_BP[[17]], title = "groupGO, Biological Process, Bicluster 6 of 10")
barplot(ggo_BP[[18]], title = "groupGO, Biological Process, Bicluster 7 of 10")
barplot(ggo_BP[[19]], title = "groupGO, Biological Process, Bicluster 8 of 10")
barplot(ggo_BP[[20]], title = "groupGO, Biological Process, Bicluster 9 of 10")
barplot(ggo_BP[[21]], title = "groupGO, Biological Process, Bicluster 10 of 10")
barplot(ggo_CC[[1]], title = "groupGO, Cellular Component, Bicluster 1 of 1")
barplot(ggo_CC[[2]], title = "groupGO, Cellular Component, Bicluster 1 of 2")
barplot(ggo_CC[[3]], title = "groupGO, Cellular Component, Bicluster 2 of 2")
barplot(ggo_CC[[4]], title = "groupGO, Cellular Component, Bicluster 1 of 3")
barplot(ggo_CC[[5]], title = "groupGO, Cellular Component, Bicluster 2 of 3")
barplot(ggo_CC[[6]], title = "groupGO, Cellular Component, Bicluster 3 of 3")
barplot(ggo_CC[[7]], title = "groupGO, Cellular Component, Bicluster 1 of 5")
barplot(ggo_CC[[8]], title = "groupGO, Cellular Component, Bicluster 2 of 5")
barplot(ggo_CC[[9]], title = "groupGO, Cellular Component, Bicluster 3 of 5")
barplot(ggo_CC[[10]], title = "groupGO, Cellular Component, Bicluster 4 of 5")
barplot(ggo_CC[[11]], title = "groupGO, Cellular Component, Bicluster 5 of 5")
barplot(ggo_CC[[12]], title = "groupGO, Cellular Component, Bicluster 1 of 10")
barplot(ggo_CC[[13]], title = "groupGO, Cellular Component, Bicluster 2 of 10")
barplot(ggo_CC[[14]], title = "groupGO, Cellular Component, Bicluster 3 of 10")
barplot(ggo_CC[[15]], title = "groupGO, Cellular Component, Bicluster 4 of 10")
barplot(ggo_CC[[16]], title = "groupGO, Cellular Component, Bicluster 5 of 10")
barplot(ggo_CC[[17]], title = "groupGO, Cellular Component, Bicluster 6 of 10")
barplot(ggo_CC[[18]], title = "groupGO, Cellular Component, Bicluster 7 of 10")
barplot(ggo_CC[[19]], title = "groupGO, Cellular Component, Bicluster 8 of 10")
barplot(ggo_CC[[20]], title = "groupGO, Cellular Component, Bicluster 9 of 10")
barplot(ggo_CC[[21]], title = "groupGO, Cellular Component, Bicluster 10 of 10")
B. GO Over-Representation
ego_MF <- list()#GO enrichment of a geneset for Molecular Function
ego_BP <- list()#GO enrichment of a geneset for Biological Process
ego_CC <- list()#GO enrichment of a geneset for Cellular Component
for(z in 1:length(geneNames)){
print(z)
input <- geneNames[[z]]
ego_MF[[z]] <- enrichGO(
gene = input,
OrgDb = org.Hs.eg.db,
ont = "MF",
pAdjustMethod = "BH",
keyType="SYMBOL",
pvalueCutoff = 0.05,
qvalueCutoff = 0.05,
minGSSize = 2,
readable = TRUE)
ego_BP[[z]] <- enrichGO(
gene = input,
OrgDb = org.Hs.eg.db,
ont = "BP",
pAdjustMethod = "BH",
keyType="SYMBOL",
pvalueCutoff = 0.05,
qvalueCutoff = 0.05,
minGSSize = 2,
readable = TRUE)
ego_CC[[z]] <- enrichGO(
gene = input,
OrgDb = org.Hs.eg.db,
ont = "CC",
pAdjustMethod = "BH",
keyType="SYMBOL",
pvalueCutoff = 0.05,
qvalueCutoff = 0.05,
minGSSize = 2,
readable = TRUE)
}## [1] 1
## [1] 2
## [1] 3
## [1] 4
## [1] 5
## [1] 6
## [1] 7
## [1] 8
## [1] 9
## [1] 10
## [1] 11
## [1] 12
## [1] 13
## [1] 14
## [1] 15
## [1] 16## --> No gene can be mapped....## --> Expected input gene ID: XRCC1,RBBP8,MRE11,TMTC4,DPM1,PIGZ## --> return NULL...## --> No gene can be mapped....## --> Expected input gene ID: LZTFL1,OR10J1,ZSCAN2,PAFAH1B1,KITLG,DMRTB1## --> return NULL...## --> No gene can be mapped....## --> Expected input gene ID: ERCC1,MAP3K7,MBD3,HDAC8,TAF6,TADA1## --> return NULL...## [1] 17
## [1] 18
## [1] 19
## [1] 20
## [1] 21for(z in 1:length(geneNames)){
print(head(ego_MF[[z]]))
print(head(ego_BP[[z]]))
print(head(ego_CC[[z]]))
}## ID Description
## GO:0106310 GO:0106310 protein serine kinase activity
## GO:0004674 GO:0004674 protein serine/threonine kinase activity
## GO:0004707 GO:0004707 MAP kinase activity
## GO:0070064 GO:0070064 proline-rich region binding
## GO:0042826 GO:0042826 histone deacetylase binding
## GO:0030291 GO:0030291 protein serine/threonine kinase inhibitor activity
## GeneRatio BgRatio pvalue p.adjust qvalue
## GO:0106310 5/24 363/18522 0.0000879512 0.009839616 0.004097469
## GO:0004674 5/24 427/18522 0.0001882293 0.009839616 0.004097469
## GO:0004707 2/24 16/18522 0.0001909646 0.009839616 0.004097469
## GO:0070064 2/24 17/18522 0.0002162553 0.009839616 0.004097469
## GO:0042826 3/24 128/18522 0.0005867501 0.021357704 0.008893896
## GO:0030291 2/24 37/18522 0.0010423909 0.024142433 0.010053529
## geneID Count
## GO:0106310 AKT1/MTOR/MAPK8/ATM/MAPK1 5
## GO:0004674 AKT1/MTOR/MAPK8/ATM/MAPK1 5
## GO:0004707 MAPK8/MAPK1 2
## GO:0070064 CCND1/YAP1 2
## GO:0042826 HSPA1A/MAPK8/CCND1 3
## GO:0030291 AKT1/CDKN1A 2
## ID Description GeneRatio
## GO:0010631 GO:0010631 epithelial cell migration 9/24
## GO:0090132 GO:0090132 epithelium migration 9/24
## GO:0090130 GO:0090130 tissue migration 9/24
## GO:0062197 GO:0062197 cellular response to chemical stress 8/24
## GO:0071214 GO:0071214 cellular response to abiotic stimulus 8/24
## GO:0104004 GO:0104004 cellular response to environmental stimulus 8/24
## BgRatio pvalue p.adjust qvalue
## GO:0010631 375/18888 4.378338e-10 3.493448e-07 1.434282e-07
## GO:0090132 378/18888 4.697252e-10 3.493448e-07 1.434282e-07
## GO:0090130 383/18888 5.274456e-10 3.493448e-07 1.434282e-07
## GO:0062197 311/18888 2.888334e-09 1.434780e-06 5.890681e-07
## GO:0071214 334/18888 5.054206e-09 1.495343e-06 6.139332e-07
## GO:0104004 334/18888 5.054206e-09 1.495343e-06 6.139332e-07
## geneID Count
## GO:0010631 AKT1/MTOR/MYH9/PTEN/PTK2/ETS1/STAT5A/ITGA2/ANLN 9
## GO:0090132 AKT1/MTOR/MYH9/PTEN/PTK2/ETS1/STAT5A/ITGA2/ANLN 9
## GO:0090130 AKT1/MTOR/MYH9/PTEN/PTK2/ETS1/STAT5A/ITGA2/ANLN 9
## GO:0062197 HSPA1A/AKT1/MTOR/MAPK8/FOXO3/ATM/MAPK1/G6PD 8
## GO:0071214 MTOR/MAPK8/CDKN1A/ATM/CASP8/PTEN/YAP1/ITGA2 8
## GO:0104004 MTOR/MAPK8/CDKN1A/ATM/CASP8/PTEN/YAP1/ITGA2 8
## ID Description GeneRatio BgRatio
## GO:0005925 GO:0005925 focal adhesion 7/24 421/19894
## GO:0030055 GO:0030055 cell-substrate junction 7/24 431/19894
## GO:0005826 GO:0005826 actomyosin contractile ring 2/24 4/19894
## GO:0009898 GO:0009898 cytoplasmic side of plasma membrane 4/24 161/19894
## GO:0070938 GO:0070938 contractile ring 2/24 10/19894
## GO:0098562 GO:0098562 cytoplasmic side of membrane 4/24 199/19894
## pvalue p.adjust qvalue
## GO:0005925 4.585265e-07 3.409715e-05 1.921762e-05
## GO:0030055 5.369630e-07 3.409715e-05 1.921762e-05
## GO:0005826 8.356555e-06 3.537608e-04 1.993845e-04
## GO:0009898 3.869971e-05 1.228716e-03 6.925211e-04
## GO:0070938 6.239748e-05 1.584896e-03 8.932692e-04
## GO:0098562 8.823680e-05 1.867679e-03 1.052650e-03
## geneID Count
## GO:0005925 HSPA1A/MYH9/KRAS/PTK2/ITGA2/MAPK1/TGM2 7
## GO:0030055 HSPA1A/MYH9/KRAS/PTK2/ITGA2/MAPK1/TGM2 7
## GO:0005826 MYH9/ANLN 2
## GO:0009898 MYH9/PTEN/KRAS/G6PD 4
## GO:0070938 MYH9/ANLN 2
## GO:0098562 MYH9/PTEN/KRAS/G6PD 4
## ID Description GeneRatio
## GO:0019903 GO:0019903 protein phosphatase binding 5/26
## GO:0140297 GO:0140297 DNA-binding transcription factor binding 7/26
## GO:0019902 GO:0019902 phosphatase binding 5/26
## GO:0001221 GO:0001221 transcription coregulator binding 4/26
## GO:0016922 GO:0016922 nuclear receptor binding 4/26
## GO:0001222 GO:0001222 transcription corepressor binding 3/26
## BgRatio pvalue p.adjust qvalue
## GO:0019903 142/18522 1.425899e-06 0.0002965870 0.0001380871
## GO:0140297 478/18522 3.136151e-06 0.0003261597 0.0001518557
## GO:0019902 189/18522 5.798930e-06 0.0004020591 0.0001871935
## GO:0001221 114/18522 1.832807e-05 0.0009530599 0.0004437323
## GO:0016922 136/18522 3.667174e-05 0.0010300946 0.0004795987
## GO:0001222 47/18522 3.821623e-05 0.0010300946 0.0004795987
## geneID Count
## GO:0019903 MET/BCL2/MAPK8/PTK2/CTNNB1 5
## GO:0140297 ESR1/BCL2/ETS1/ARID1A/YWHAZ/NCOA3/CTNNB1 7
## GO:0019902 MET/BCL2/MAPK8/PTK2/CTNNB1 5
## GO:0001221 ESR1/ETS1/FOXO3/CTNNB1 4
## GO:0016922 ESR1/ARID1A/NCOA3/CTNNB1 4
## GO:0001222 ESR1/ETS1/CTNNB1 3
## ID Description
## GO:0051402 GO:0051402 neuron apoptotic process
## GO:2000045 GO:2000045 regulation of G1/S transition of mitotic cell cycle
## GO:1902806 GO:1902806 regulation of cell cycle G1/S phase transition
## GO:1901990 GO:1901990 regulation of mitotic cell cycle phase transition
## GO:0000082 GO:0000082 G1/S transition of mitotic cell cycle
## GO:0043523 GO:0043523 regulation of neuron apoptotic process
## GeneRatio BgRatio pvalue p.adjust qvalue
## GO:0051402 9/26 292/18888 1.106898e-10 2.477237e-07 9.798956e-08
## GO:2000045 7/26 185/18888 4.338048e-09 4.854276e-06 1.920157e-06
## GO:1902806 7/26 211/18888 1.079622e-08 8.053980e-06 3.185832e-06
## GO:1901990 8/26 356/18888 1.710620e-08 9.570921e-06 3.785873e-06
## GO:0000082 7/26 234/18888 2.204334e-08 9.866597e-06 3.902831e-06
## GO:0043523 7/26 244/18888 2.939457e-08 1.096418e-05 4.336988e-06
## geneID Count
## GO:0051402 G6PD/BCL2/KRAS/CCND1/XIAP/BID/ATM/FOXO3/CTNNB1 9
## GO:2000045 BCL2/CCND1/AKT1/ARID1A/BID/PTEN/ATM 7
## GO:1902806 BCL2/CCND1/AKT1/ARID1A/BID/PTEN/ATM 7
## GO:1901990 BCL2/CCND1/AKT1/ARID1A/BID/PTEN/ATM/CHEK1 8
## GO:0000082 BCL2/CCND1/AKT1/ARID1A/BID/PTEN/ATM 7
## GO:0043523 G6PD/BCL2/KRAS/CCND1/ATM/FOXO3/CTNNB1 7
## ID Description
## GO:0017053 GO:0017053 transcription repressor complex
## GO:0090571 GO:0090571 RNA polymerase II transcription repressor complex
## GO:0005741 GO:0005741 mitochondrial outer membrane
## GO:0005925 GO:0005925 focal adhesion
## GO:0030055 GO:0030055 cell-substrate junction
## GO:0031968 GO:0031968 organelle outer membrane
## GeneRatio BgRatio pvalue p.adjust qvalue
## GO:0017053 3/26 77/19894 0.0001359483 0.005897502 0.0033461
## GO:0090571 2/26 15/19894 0.0001706628 0.005897502 0.0033461
## GO:0005741 4/26 219/19894 0.0001766044 0.005897502 0.0033461
## GO:0005925 5/26 421/19894 0.0001888698 0.005897502 0.0033461
## GO:0030055 5/26 431/19894 0.0002106347 0.005897502 0.0033461
## GO:0031968 4/26 248/19894 0.0002839739 0.005897502 0.0033461
## geneID Count
## GO:0017053 CCND1/FOXO3/CTNNB1 3
## GO:0090571 FOXO3/CTNNB1 2
## GO:0005741 BCL2/KRAS/BID/FOXO3 4
## GO:0005925 KRAS/PTK2/YWHAZ/ITGA2/CTNNB1 5
## GO:0030055 KRAS/PTK2/YWHAZ/ITGA2/CTNNB1 5
## GO:0031968 BCL2/KRAS/BID/FOXO3 4
## ID Description GeneRatio
## GO:0031625 GO:0031625 ubiquitin protein ligase binding 7/39
## GO:0044389 GO:0044389 ubiquitin-like protein ligase binding 7/39
## GO:0097718 GO:0097718 disordered domain specific binding 3/39
## GO:0051219 GO:0051219 phosphoprotein binding 4/39
## GO:0043559 GO:0043559 insulin binding 2/39
## GO:0140297 GO:0140297 DNA-binding transcription factor binding 7/39
## BgRatio pvalue p.adjust qvalue
## GO:0031625 305/18522 2.999855e-06 0.0006097502 0.0002586178
## GO:0044389 324/18522 4.467034e-06 0.0006097502 0.0002586178
## GO:0097718 32/18522 4.103709e-05 0.0023493747 0.0009964574
## GO:0051219 93/18522 4.281994e-05 0.0023493747 0.0009964574
## GO:0043559 5/18522 4.302884e-05 0.0023493747 0.0009964574
## GO:0140297 478/18522 5.486105e-05 0.0024961776 0.0010587219
## geneID Count
## GO:0031625 RB1/HSPA1A/BID/CDKN1A/CASP8/TUBA1B/SQSTM1 7
## GO:0044389 RB1/HSPA1A/BID/CDKN1A/CASP8/TUBA1B/SQSTM1 7
## GO:0097718 RB1/HSPA1A/NCOA3 3
## GO:0051219 RB1/MTOR/PIK3R1/MAPK1 4
## GO:0043559 PIK3R1/IGF1R 2
## GO:0140297 RB1/VHL/ETS1/ARID1A/STAT5A/NCOA3/YAP1 7
## ID Description
## GO:0030099 GO:0030099 myeloid cell differentiation
## GO:0071214 GO:0071214 cellular response to abiotic stimulus
## GO:0104004 GO:0104004 cellular response to environmental stimulus
## GO:1901990 GO:1901990 regulation of mitotic cell cycle phase transition
## GO:2000045 GO:2000045 regulation of G1/S transition of mitotic cell cycle
## GO:0051402 GO:0051402 neuron apoptotic process
## GeneRatio BgRatio pvalue p.adjust qvalue
## GO:0030099 13/39 439/18888 2.271039e-12 5.339213e-09 2.471847e-09
## GO:0071214 11/39 334/18888 4.834683e-11 3.788780e-08 1.754057e-08
## GO:0104004 11/39 334/18888 4.834683e-11 3.788780e-08 1.754057e-08
## GO:1901990 10/39 356/18888 1.950902e-09 1.146642e-06 5.308506e-07
## GO:2000045 8/39 185/18888 3.454398e-09 1.624258e-06 7.519679e-07
## GO:0051402 9/39 292/18888 6.294494e-09 2.466393e-06 1.141843e-06
## geneID
## GO:0030099 RB1/HSPA1A/MTOR/ETS1/MYH9/FOXO3/CASP8/PIK3R1/STAT5A/GAB2/G6PD/RBM15/FASN
## GO:0071214 MTOR/MAPK8/CDKN1A/ATM/CASP8/PTEN/PIK3R1/CHEK1/IGF1R/YAP1/ITGA2
## GO:0104004 MTOR/MAPK8/CDKN1A/ATM/CASP8/PTEN/PIK3R1/CHEK1/IGF1R/YAP1/ITGA2
## GO:1901990 RB1/AKT1/ARID1A/BID/CDKN1A/ATM/PTEN/CCND1/CHEK1/ANLN
## GO:2000045 RB1/AKT1/ARID1A/BID/CDKN1A/ATM/PTEN/CCND1
## GO:0051402 RB1/XIAP/BID/FOXO3/ATM/CASP8/KRAS/CCND1/G6PD
## Count
## GO:0030099 13
## GO:0071214 11
## GO:0104004 11
## GO:1901990 10
## GO:2000045 8
## GO:0051402 9
## ID Description GeneRatio BgRatio
## GO:0005925 GO:0005925 focal adhesion 7/39 421/19894
## GO:0030055 GO:0030055 cell-substrate junction 7/39 431/19894
## GO:0005826 GO:0005826 actomyosin contractile ring 2/39 4/19894
## GO:0016605 GO:0016605 PML body 4/39 108/19894
## GO:0005741 GO:0005741 mitochondrial outer membrane 5/39 219/19894
## GO:0031968 GO:0031968 organelle outer membrane 5/39 248/19894
## pvalue p.adjust qvalue
## GO:0005925 1.549331e-05 0.001382133 0.0007549631
## GO:0030055 1.802378e-05 0.001382133 0.0007549631
## GO:0005826 2.241297e-05 0.001382133 0.0007549631
## GO:0016605 5.836022e-05 0.002425454 0.0013248570
## GO:0005741 6.555282e-05 0.002425454 0.0013248570
## GO:0031968 1.177667e-04 0.003231777 0.0017652951
## geneID Count
## GO:0005925 HSPA1A/MYH9/KRAS/PTK2/ITGA2/MAPK1/TGM2 7
## GO:0030055 HSPA1A/MYH9/KRAS/PTK2/ITGA2/MAPK1/TGM2 7
## GO:0005826 MYH9/ANLN 2
## GO:0016605 RB1/MTOR/PTEN/SQSTM1 4
## GO:0005741 MTOR/BID/FOXO3/CASP8/KRAS 5
## GO:0031968 MTOR/BID/FOXO3/CASP8/KRAS 5
## ID Description GeneRatio
## GO:0140297 GO:0140297 DNA-binding transcription factor binding 10/44
## GO:0019902 GO:0019902 phosphatase binding 7/44
## GO:0031625 GO:0031625 ubiquitin protein ligase binding 8/44
## GO:0044389 GO:0044389 ubiquitin-like protein ligase binding 8/44
## GO:0019903 GO:0019903 protein phosphatase binding 6/44
## GO:0019887 GO:0019887 protein kinase regulator activity 7/44
## BgRatio pvalue p.adjust qvalue
## GO:0140297 478/18522 1.347502e-07 3.907755e-05 1.673739e-05
## GO:0019902 189/18522 2.870435e-07 4.162131e-05 1.782691e-05
## GO:0031625 305/18522 5.222688e-07 5.048598e-05 2.162376e-05
## GO:0044389 324/18522 8.238420e-07 5.516999e-05 2.362998e-05
## GO:0019903 142/18522 1.014288e-06 5.516999e-05 2.362998e-05
## GO:0019887 232/18522 1.141448e-06 5.516999e-05 2.362998e-05
## geneID Count
## GO:0140297 ESR1/BCL2/VHL/ETS1/PARP1/YWHAZ/STAT5A/MYC/YAP1/CTNNB1 10
## GO:0019902 MET/BCL2/MAPK8/PTK2/MAPK1/CDH2/CTNNB1 7
## GO:0031625 BCL2/HSPA1A/CDKN1A/CASP8/PARP1/YWHAZ/ERBB3/CTNNB1 8
## GO:0044389 BCL2/HSPA1A/CDKN1A/CASP8/PARP1/YWHAZ/ERBB3/CTNNB1 8
## GO:0019903 MET/BCL2/MAPK8/PTK2/CDH2/CTNNB1 6
## GO:0019887 CCND1/AKT1/CDKN1A/CCNE2/CASP3/PIK3CA/ERBB3 7
## ID Description GeneRatio
## GO:0043523 GO:0043523 regulation of neuron apoptotic process 13/44
## GO:0071214 GO:0071214 cellular response to abiotic stimulus 14/44
## GO:0104004 GO:0104004 cellular response to environmental stimulus 14/44
## GO:0051402 GO:0051402 neuron apoptotic process 13/44
## GO:0048732 GO:0048732 gland development 14/44
## GO:0001667 GO:0001667 ameboidal-type cell migration 14/44
## BgRatio pvalue p.adjust qvalue
## GO:0043523 244/18888 7.372691e-15 1.499850e-11 6.010986e-12
## GO:0071214 334/18888 1.587702e-14 1.499850e-11 6.010986e-12
## GO:0104004 334/18888 1.587702e-14 1.499850e-11 6.010986e-12
## GO:0051402 292/18888 7.463526e-14 5.287908e-11 2.119248e-11
## GO:0048732 449/18888 9.024913e-13 5.115321e-10 2.050080e-10
## GO:0001667 498/18888 3.645943e-12 1.713589e-09 6.867596e-10
## geneID
## GO:0043523 G6PD/BCL2/KRAS/CCND1/FOXO3/ATM/CASP8/PARP1/CASP3/BCL2L11/PIK3CA/ERBB3/CTNNB1
## GO:0071214 IGF1R/MTOR/MAPK8/CDKN1A/ATM/CASP8/PTEN/PARP1/MYC/CASP3/YAP1/CHEK1/ITGA2/PIK3CA
## GO:0104004 IGF1R/MTOR/MAPK8/CDKN1A/ATM/CASP8/PTEN/PARP1/MYC/CASP3/YAP1/CHEK1/ITGA2/PIK3CA
## GO:0051402 G6PD/BCL2/KRAS/CCND1/FOXO3/ATM/CASP8/PARP1/CASP3/BCL2L11/PIK3CA/ERBB3/CTNNB1
## GO:0048732 ESR1/MET/BCL2/CCND1/AKT1/ATM/STAT5A/BCL2L11/ITGA2/PIK3CA/MAPK1/SRSF1/CTNNB1/TGM2
## GO:0001667 MET/AKT1/MTOR/MYH9/PTEN/PTK2/ETS1/RAB25/STAT5A/FN1/ITGA2/PIK3CA/ANLN/CDH2
## Count
## GO:0043523 13
## GO:0071214 14
## GO:0104004 14
## GO:0051402 13
## GO:0048732 14
## GO:0001667 14
## ID Description
## GO:0005925 GO:0005925 focal adhesion
## GO:0030055 GO:0030055 cell-substrate junction
## GO:0090571 GO:0090571 RNA polymerase II transcription repressor complex
## GO:0005741 GO:0005741 mitochondrial outer membrane
## GO:0031968 GO:0031968 organelle outer membrane
## GO:0019867 GO:0019867 outer membrane
## GeneRatio BgRatio pvalue p.adjust qvalue
## GO:0005925 10/44 421/19894 2.113139e-08 2.676647e-06 1.263028e-06
## GO:0030055 10/44 431/19894 2.637091e-08 2.676647e-06 1.263028e-06
## GO:0090571 3/44 15/19894 4.508384e-06 3.050673e-04 1.439519e-04
## GO:0005741 6/44 219/19894 8.272627e-06 4.198358e-04 1.981077e-04
## GO:0031968 6/44 248/19894 1.677033e-05 5.937494e-04 2.801721e-04
## GO:0019867 6/44 250/19894 1.754924e-05 5.937494e-04 2.801721e-04
## geneID Count
## GO:0005925 KRAS/HSPA1A/MYH9/PTK2/YWHAZ/ITGA2/MAPK1/CDH2/CTNNB1/TGM2 10
## GO:0030055 KRAS/HSPA1A/MYH9/PTK2/YWHAZ/ITGA2/MAPK1/CDH2/CTNNB1/TGM2 10
## GO:0090571 FOXO3/MYC/CTNNB1 3
## GO:0005741 BCL2/KRAS/MTOR/FOXO3/CASP8/BCL2L11 6
## GO:0031968 BCL2/KRAS/MTOR/FOXO3/CASP8/BCL2L11 6
## GO:0019867 BCL2/KRAS/MTOR/FOXO3/CASP8/BCL2L11 6
## ID
## GO:0043559 GO:0043559
## GO:0120283 GO:0120283
## GO:0043560 GO:0043560
## GO:0140993 GO:0140993
## GO:0004707 GO:0004707
## GO:0005068 GO:0005068
## Description
## GO:0043559 insulin binding
## GO:0120283 protein serine/threonine kinase binding
## GO:0043560 insulin receptor substrate binding
## GO:0140993 histone modifying activity
## GO:0004707 MAP kinase activity
## GO:0005068 transmembrane receptor protein tyrosine kinase adaptor activity
## GeneRatio BgRatio pvalue p.adjust qvalue
## GO:0043559 2/26 5/18522 1.889884e-05 0.003458487 0.001511907
## GO:0120283 2/26 7/18522 3.961902e-05 0.003625141 0.001584761
## GO:0043560 2/26 13/18522 1.463956e-04 0.006650055 0.002907128
## GO:0140993 4/26 207/18522 1.868027e-04 0.006650055 0.002907128
## GO:0004707 2/26 16/18522 2.246413e-04 0.006650055 0.002907128
## GO:0005068 2/26 17/18522 2.543737e-04 0.006650055 0.002907128
## geneID Count
## GO:0043559 PIK3R1/IGF1R 2
## GO:0120283 XIAP/MAPK8 2
## GO:0043560 PIK3R1/IGF1R 2
## GO:0140993 ATM/CHEK1/NCOA3/TGM2 4
## GO:0004707 MAPK8/MAPK1 2
## GO:0005068 PIK3R1/GAB2 2
## ID Description GeneRatio
## GO:0030099 GO:0030099 myeloid cell differentiation 9/26
## GO:0071214 GO:0071214 cellular response to abiotic stimulus 8/26
## GO:0104004 GO:0104004 cellular response to environmental stimulus 8/26
## GO:0051402 GO:0051402 neuron apoptotic process 7/26
## GO:0042770 GO:0042770 signal transduction in response to DNA damage 6/26
## GO:0071496 GO:0071496 cellular response to external stimulus 7/26
## BgRatio pvalue p.adjust qvalue
## GO:0030099 439/18888 4.013892e-09 5.458224e-06 2.662727e-06
## GO:0071214 334/18888 1.040984e-08 5.458224e-06 2.662727e-06
## GO:0104004 334/18888 1.040984e-08 5.458224e-06 2.662727e-06
## GO:0051402 292/18888 1.004486e-07 3.950139e-05 1.927026e-05
## GO:0042770 188/18888 1.751351e-07 5.509752e-05 2.687864e-05
## GO:0071496 335/18888 2.552859e-07 6.692746e-05 3.264973e-05
## geneID Count
## GO:0030099 ETS1/MYH9/FOXO3/CASP8/PIK3R1/STAT5A/GAB2/G6PD/FASN 9
## GO:0071214 MAPK8/CDKN1A/ATM/CASP8/PIK3R1/CHEK1/IGF1R/YAP1 8
## GO:0104004 MAPK8/CDKN1A/ATM/CASP8/PIK3R1/CHEK1/IGF1R/YAP1 8
## GO:0051402 XIAP/BID/FOXO3/ATM/CASP8/CCND1/G6PD 7
## GO:0042770 BID/CDKN1A/FOXO3/ATM/CCND1/CHEK1 6
## GO:0071496 MAPK8/CDKN1A/FOXO3/CASP8/CHEK1/IGF1R/MAPK1 7
## ID
## GO:0005826 GO:0005826
## GO:0070938 GO:0070938
## GO:0061695 GO:0061695
## GO:1902911 GO:1902911
## GO:0000307 GO:0000307
## GO:0070557 GO:0070557
## Description
## GO:0005826 actomyosin contractile ring
## GO:0070938 contractile ring
## GO:0061695 transferase complex, transferring phosphorus-containing groups
## GO:1902911 protein kinase complex
## GO:0000307 cyclin-dependent protein kinase holoenzyme complex
## GO:0070557 PCNA-p21 complex
## GeneRatio BgRatio pvalue p.adjust qvalue
## GO:0005826 2/26 4/19894 9.838827e-06 0.001180659 0.0006524696
## GO:0070938 2/26 10/19894 7.343589e-05 0.004406154 0.0024349797
## GO:0061695 4/26 308/19894 6.436502e-04 0.025746006 0.0142280561
## GO:1902911 3/26 150/19894 9.618296e-04 0.028854888 0.0159461221
## GO:0000307 2/26 56/19894 2.421991e-03 0.032954906 0.0182119217
## GO:0070557 1/26 2/19894 2.612211e-03 0.032954906 0.0182119217
## geneID Count
## GO:0005826 MYH9/ANLN 2
## GO:0070938 MYH9/ANLN 2
## GO:0061695 CDKN1A/CCND1/PIK3R1/IGF1R 4
## GO:1902911 CDKN1A/CCND1/IGF1R 3
## GO:0000307 CDKN1A/CCND1 2
## GO:0070557 CDKN1A 1
## ID
## GO:0140297 GO:0140297
## GO:0001221 GO:0001221
## GO:0061629 GO:0061629
## GO:0016922 GO:0016922
## GO:0001222 GO:0001222
## GO:0019903 GO:0019903
## Description
## GO:0140297 DNA-binding transcription factor binding
## GO:0001221 transcription coregulator binding
## GO:0061629 RNA polymerase II-specific DNA-binding transcription factor binding
## GO:0016922 nuclear receptor binding
## GO:0001222 transcription corepressor binding
## GO:0019903 protein phosphatase binding
## GeneRatio BgRatio pvalue p.adjust qvalue
## GO:0140297 8/23 478/18522 6.472171e-08 1.106741e-05 4.837096e-06
## GO:0001221 5/23 114/18522 2.490429e-07 2.129317e-05 9.306340e-06
## GO:0061629 6/23 343/18522 2.986564e-06 1.702342e-04 7.440213e-05
## GO:0016922 4/23 136/18522 2.209533e-05 6.596016e-04 2.882838e-04
## GO:0001222 3/23 47/18522 2.617056e-05 6.596016e-04 2.882838e-04
## GO:0019903 4/23 142/18522 2.618056e-05 6.596016e-04 2.882838e-04
## geneID Count
## GO:0140297 ESR1/BCL2/ETS1/ARID1A/YWHAZ/NCOA3/CTNNB1/GATA3 8
## GO:0001221 ESR1/ETS1/FOXO3/CTNNB1/GATA3 5
## GO:0061629 ESR1/ETS1/ARID1A/NCOA3/CTNNB1/GATA3 6
## GO:0016922 ESR1/ARID1A/NCOA3/CTNNB1 4
## GO:0001222 ESR1/ETS1/CTNNB1 3
## GO:0019903 MET/BCL2/MAPK8/CTNNB1 4
## ID Description GeneRatio
## GO:0051402 GO:0051402 neuron apoptotic process 9/23
## GO:0048872 GO:0048872 homeostasis of number of cells 8/23
## GO:0043523 GO:0043523 regulation of neuron apoptotic process 7/23
## GO:1904019 GO:1904019 epithelial cell apoptotic process 6/23
## GO:1902893 GO:1902893 regulation of miRNA transcription 5/23
## GO:0061614 GO:0061614 miRNA transcription 5/23
## BgRatio pvalue p.adjust qvalue
## GO:0051402 292/18888 3.015195e-11 6.310803e-08 2.501025e-08
## GO:0048872 322/18888 2.567372e-09 2.686755e-06 1.064784e-06
## GO:0043523 244/18888 1.132333e-08 7.899909e-06 3.130801e-06
## GO:1904019 147/18888 1.815405e-08 9.499105e-06 3.764576e-06
## GO:1902893 75/18888 2.743477e-08 1.023597e-05 4.056601e-06
## GO:0061614 76/18888 2.934343e-08 1.023597e-05 4.056601e-06
## geneID Count
## GO:0051402 G6PD/BCL2/KRAS/CCND1/XIAP/BID/FOXO3/CTNNB1/GATA3 9
## GO:0048872 G6PD/BCL2/KRAS/AKT1/ETS1/XIAP/FOXO3/GATA3 8
## GO:0043523 G6PD/BCL2/KRAS/CCND1/FOXO3/CTNNB1/GATA3 7
## GO:1904019 ESR1/BCL2/IGF1R/BID/FOXO3/GATA3 6
## GO:1902893 ESR1/NOTCH3/ETS1/FOXO3/GATA3 5
## GO:0061614 ESR1/NOTCH3/ETS1/FOXO3/GATA3 5
## ID Description
## GO:0017053 GO:0017053 transcription repressor complex
## GO:0005741 GO:0005741 mitochondrial outer membrane
## GO:0090571 GO:0090571 RNA polymerase II transcription repressor complex
## GO:0031968 GO:0031968 organelle outer membrane
## GO:0019867 GO:0019867 outer membrane
## GO:0000791 GO:0000791 euchromatin
## GeneRatio BgRatio pvalue p.adjust qvalue
## GO:0017053 3/23 77/19894 9.337874e-05 0.004144173 0.002293961
## GO:0005741 4/23 219/19894 1.073470e-04 0.004144173 0.002293961
## GO:0090571 2/23 15/19894 1.330282e-04 0.004144173 0.002293961
## GO:0031968 4/23 248/19894 1.732117e-04 0.004144173 0.002293961
## GO:0019867 4/23 250/19894 1.786281e-04 0.004144173 0.002293961
## GO:0000791 2/23 61/19894 2.244738e-03 0.026807326 0.014838901
## geneID Count
## GO:0017053 CCND1/FOXO3/CTNNB1 3
## GO:0005741 BCL2/KRAS/BID/FOXO3 4
## GO:0090571 FOXO3/CTNNB1 2
## GO:0031968 BCL2/KRAS/BID/FOXO3 4
## GO:0019867 BCL2/KRAS/BID/FOXO3 4
## GO:0000791 ESR1/CTNNB1 2
## ID Description GeneRatio BgRatio
## GO:0031625 GO:0031625 ubiquitin protein ligase binding 7/40 305/18522
## GO:0044389 GO:0044389 ubiquitin-like protein ligase binding 7/40 324/18522
## GO:0097718 GO:0097718 disordered domain specific binding 3/40 32/18522
## GO:0043125 GO:0043125 ErbB-3 class receptor binding 2/40 5/18522
## GO:0043559 GO:0043559 insulin binding 2/40 5/18522
## GO:0051219 GO:0051219 phosphoprotein binding 4/40 93/18522
## pvalue p.adjust qvalue
## GO:0031625 3.585287e-06 0.0007227572 0.0003060032
## GO:0044389 5.334001e-06 0.0007227572 0.0003060032
## GO:0097718 4.431239e-05 0.0021406983 0.0009063357
## GO:0043125 4.528862e-05 0.0021406983 0.0009063357
## GO:0043559 4.528862e-05 0.0021406983 0.0009063357
## GO:0051219 4.739553e-05 0.0021406983 0.0009063357
## geneID Count
## GO:0031625 RB1/HSPA1A/BID/CDKN1A/CASP8/TUBA1B/ERBB3 7
## GO:0044389 RB1/HSPA1A/BID/CDKN1A/CASP8/TUBA1B/ERBB3 7
## GO:0097718 RB1/HSPA1A/NCOA3 3
## GO:0043125 PIK3R1/ERBB3 2
## GO:0043559 PIK3R1/IGF1R 2
## GO:0051219 RB1/MTOR/PIK3R1/MAPK1 4
## ID Description
## GO:0071214 GO:0071214 cellular response to abiotic stimulus
## GO:0104004 GO:0104004 cellular response to environmental stimulus
## GO:0030099 GO:0030099 myeloid cell differentiation
## GO:0051402 GO:0051402 neuron apoptotic process
## GO:0071496 GO:0071496 cellular response to external stimulus
## GO:1901990 GO:1901990 regulation of mitotic cell cycle phase transition
## GeneRatio BgRatio pvalue p.adjust qvalue
## GO:0071214 11/40 334/18888 6.564127e-11 5.226059e-08 2.416486e-08
## GO:0104004 11/40 334/18888 6.564127e-11 5.226059e-08 2.416486e-08
## GO:0030099 12/40 439/18888 6.634861e-11 5.226059e-08 2.416486e-08
## GO:0051402 10/40 292/18888 3.763509e-10 2.223293e-07 1.028032e-07
## GO:0071496 10/40 335/18888 1.424577e-09 6.732551e-07 3.113076e-07
## GO:1901990 10/40 356/18888 2.557984e-09 1.007419e-06 4.658223e-07
## geneID
## GO:0071214 MTOR/MAPK8/CDKN1A/ATM/CASP8/PTEN/PIK3R1/CHEK1/IGF1R/YAP1/ITGA2
## GO:0104004 MTOR/MAPK8/CDKN1A/ATM/CASP8/PTEN/PIK3R1/CHEK1/IGF1R/YAP1/ITGA2
## GO:0030099 RB1/HSPA1A/MTOR/ETS1/MYH9/FOXO3/CASP8/PIK3R1/STAT5A/GAB2/G6PD/FASN
## GO:0051402 RB1/XIAP/BID/FOXO3/ATM/CASP8/KRAS/CCND1/ERBB3/G6PD
## GO:0071496 MTOR/MAPK8/CDKN1A/FOXO3/CASP8/CHEK1/IGF1R/ITGA2/MAPK1/TSC1
## GO:1901990 RB1/AKT1/ARID1A/BID/CDKN1A/ATM/PTEN/CCND1/CHEK1/ANLN
## Count
## GO:0071214 11
## GO:0104004 11
## GO:0030099 12
## GO:0051402 10
## GO:0071496 10
## GO:1901990 10
## ID Description GeneRatio BgRatio
## GO:0005925 GO:0005925 focal adhesion 7/40 421/19894
## GO:0030055 GO:0030055 cell-substrate junction 7/40 431/19894
## GO:0005826 GO:0005826 actomyosin contractile ring 2/40 4/19894
## GO:0005741 GO:0005741 mitochondrial outer membrane 5/40 219/19894
## GO:0031968 GO:0031968 organelle outer membrane 5/40 248/19894
## GO:0019867 GO:0019867 outer membrane 5/40 250/19894
## pvalue p.adjust qvalue
## GO:0005925 1.844060e-05 0.001368279 0.0007284243
## GO:0030055 2.144302e-05 0.001368279 0.0007284243
## GO:0005826 2.359102e-05 0.001368279 0.0007284243
## GO:0005741 7.425089e-05 0.003229914 0.0017194942
## GO:0031968 1.332324e-04 0.004011594 0.0021356340
## GO:0019867 1.383308e-04 0.004011594 0.0021356340
## geneID Count
## GO:0005925 HSPA1A/MYH9/KRAS/PTK2/ITGA2/MAPK1/TGM2 7
## GO:0030055 HSPA1A/MYH9/KRAS/PTK2/ITGA2/MAPK1/TGM2 7
## GO:0005826 MYH9/ANLN 2
## GO:0005741 MTOR/BID/FOXO3/CASP8/KRAS 5
## GO:0031968 MTOR/BID/FOXO3/CASP8/KRAS 5
## GO:0019867 MTOR/BID/FOXO3/CASP8/KRAS 5
## ID
## GO:0016538 GO:0016538
## GO:0019887 GO:0019887
## GO:0019207 GO:0019207
## GO:0106017 GO:0106017
## GO:0031625 GO:0031625
## GO:0097199 GO:0097199
## Description
## GO:0016538 cyclin-dependent protein serine/threonine kinase regulator activity
## GO:0019887 protein kinase regulator activity
## GO:0019207 kinase regulator activity
## GO:0106017 phosphatidylinositol-3,4-bisphosphate phosphatase activity
## GO:0031625 ubiquitin protein ligase binding
## GO:0097199 cysteine-type endopeptidase activity involved in apoptotic signaling pathway
## GeneRatio BgRatio pvalue p.adjust qvalue
## GO:0016538 4/41 50/18522 4.420105e-06 0.001387913 0.0006513839
## GO:0019887 6/41 232/18522 1.128071e-05 0.001771072 0.0008312105
## GO:0019207 6/41 270/18522 2.659290e-05 0.002245393 0.0010538215
## GO:0106017 2/41 4/18522 2.860373e-05 0.002245393 0.0010538215
## GO:0031625 6/41 305/18522 5.253641e-05 0.002675883 0.0012558620
## GO:0097199 2/41 6/18522 7.130874e-05 0.002675883 0.0012558620
## geneID Count
## GO:0016538 CDKN1A/CCNE2/CCND1/CASP3 4
## GO:0019887 AKT1/CDKN1A/CCNE2/CCND1/CASP3/PIK3CA 6
## GO:0019207 AKT1/CDKN1A/CCNE2/CCND1/CASP3/PIK3CA 6
## GO:0106017 PTEN/INPP4B 2
## GO:0031625 HSPA1A/CDKN1A/CASP8/PARP1/BCL2/SQSTM1 6
## GO:0097199 CASP8/CASP3 2
## ID Description GeneRatio
## GO:0071214 GO:0071214 cellular response to abiotic stimulus 13/41
## GO:0104004 GO:0104004 cellular response to environmental stimulus 13/41
## GO:0051402 GO:0051402 neuron apoptotic process 12/41
## GO:0062197 GO:0062197 cellular response to chemical stress 12/41
## GO:0043523 GO:0043523 regulation of neuron apoptotic process 11/41
## GO:0009411 GO:0009411 response to UV 9/41
## BgRatio pvalue p.adjust qvalue
## GO:0071214 334/18888 1.478774e-13 1.890612e-10 8.187738e-11
## GO:0104004 334/18888 1.478774e-13 1.890612e-10 8.187738e-11
## GO:0051402 292/18888 7.877682e-13 6.714411e-10 2.907832e-10
## GO:0062197 311/18888 1.656663e-12 1.059022e-09 4.586342e-10
## GO:0043523 244/18888 2.996446e-12 1.532382e-09 6.636339e-10
## GO:0009411 154/18888 3.527981e-11 1.503508e-08 6.511292e-09
## geneID
## GO:0071214 MTOR/MAPK8/CDKN1A/ATM/CASP8/PTEN/PARP1/IGF1R/MYC/CASP3/YAP1/ITGA2/PIK3CA
## GO:0104004 MTOR/MAPK8/CDKN1A/ATM/CASP8/PTEN/PARP1/IGF1R/MYC/CASP3/YAP1/ITGA2/PIK3CA
## GO:0051402 FOXO3/ATM/CASP8/KRAS/PARP1/CCND1/XIAP/BCL2/CASP3/BCL2L11/PIK3CA/G6PD
## GO:0062197 HSPA1A/AKT1/MTOR/MAPK8/FOXO3/ATM/PARP1/CASP3/PIK3CA/MAPK1/G6PD/PRDX1
## GO:0043523 FOXO3/ATM/CASP8/KRAS/PARP1/CCND1/BCL2/CASP3/BCL2L11/PIK3CA/G6PD
## GO:0009411 AKT1/MAPK8/CDKN1A/PARP1/CCND1/BCL2/MYC/CASP3/MSH6
## Count
## GO:0071214 13
## GO:0104004 13
## GO:0051402 12
## GO:0062197 12
## GO:0043523 11
## GO:0009411 9
## ID Description GeneRatio BgRatio
## GO:0005741 GO:0005741 mitochondrial outer membrane 6/41 219/19894
## GO:0031968 GO:0031968 organelle outer membrane 6/41 248/19894
## GO:0019867 GO:0019867 outer membrane 6/41 250/19894
## GO:0005925 GO:0005925 focal adhesion 7/41 421/19894
## GO:0005826 GO:0005826 actomyosin contractile ring 2/41 4/19894
## GO:0030055 GO:0030055 cell-substrate junction 7/41 431/19894
## pvalue p.adjust qvalue
## GO:0005741 5.416377e-06 0.0006806263 0.0003804869
## GO:0031968 1.102118e-05 0.0006806263 0.0003804869
## GO:0019867 1.153604e-05 0.0006806263 0.0003804869
## GO:0005925 2.183569e-05 0.0007487025 0.0004185432
## GO:0005826 2.479915e-05 0.0007487025 0.0004185432
## GO:0030055 2.537974e-05 0.0007487025 0.0004185432
## geneID Count
## GO:0005741 MTOR/FOXO3/CASP8/KRAS/BCL2/BCL2L11 6
## GO:0031968 MTOR/FOXO3/CASP8/KRAS/BCL2/BCL2L11 6
## GO:0019867 MTOR/FOXO3/CASP8/KRAS/BCL2/BCL2L11 6
## GO:0005925 HSPA1A/MYH9/KRAS/PTK2/ITGA2/MAPK1/TGM2 7
## GO:0005826 MYH9/ANLN 2
## GO:0030055 HSPA1A/MYH9/KRAS/PTK2/ITGA2/MAPK1/TGM2 7
## ID
## GO:0003810 GO:0003810
## GO:0004861 GO:0004861
## GO:0140311 GO:0140311
## GO:0030332 GO:0030332
## GO:0030291 GO:0030291
## GO:0140313 GO:0140313
## Description
## GO:0003810 protein-glutamine gamma-glutamyltransferase activity
## GO:0004861 cyclin-dependent protein serine/threonine kinase inhibitor activity
## GO:0140311 protein sequestering activity
## GO:0030332 cyclin binding
## GO:0030291 protein serine/threonine kinase inhibitor activity
## GO:0140313 molecular sequestering activity
## GeneRatio BgRatio pvalue p.adjust qvalue geneID Count
## GO:0003810 1/3 9/18522 0.001457096 0.02525225 0.007156507 TGM2 1
## GO:0004861 1/3 12/18522 0.001942480 0.02525225 0.007156507 CDKN1A 1
## GO:0140311 1/3 29/18522 0.004690019 0.03000055 0.008502179 CDKN1A 1
## GO:0030332 1/3 34/18522 0.005497158 0.03000055 0.008502179 CDKN1A 1
## GO:0030291 1/3 37/18522 0.005981232 0.03000055 0.008502179 CDKN1A 1
## GO:0140313 1/3 49/18522 0.007915957 0.03000055 0.008502179 CDKN1A 1
## ID Description
## GO:0018277 GO:0018277 protein deamination
## GO:1905179 GO:1905179 negative regulation of cardiac muscle tissue regeneration
## GO:1905178 GO:1905178 regulation of cardiac muscle tissue regeneration
## GO:0060605 GO:0060605 tube lumen cavitation
## GO:0060662 GO:0060662 salivary gland cavitation
## GO:0048638 GO:0048638 regulation of developmental growth
## GeneRatio BgRatio pvalue p.adjust qvalue
## GO:0018277 1/3 2/18888 0.0003176452 0.01661722 0.002905419
## GO:1905179 1/3 2/18888 0.0003176452 0.01661722 0.002905419
## GO:1905178 1/3 4/18888 0.0006352231 0.01661722 0.002905419
## GO:0060605 1/3 5/18888 0.0007939868 0.01661722 0.002905419
## GO:0060662 1/3 5/18888 0.0007939868 0.01661722 0.002905419
## GO:0048638 2/3 330/18888 0.0009024527 0.01661722 0.002905419
## geneID Count
## GO:0018277 TGM2 1
## GO:1905179 CDKN1A 1
## GO:1905178 CDKN1A 1
## GO:0060605 TGM2 1
## GO:0060662 TGM2 1
## GO:0048638 CDKN1A/STAT5A 2
## ID Description
## GO:0070557 GO:0070557 PCNA-p21 complex
## GO:0000307 GO:0000307 cyclin-dependent protein kinase holoenzyme complex
## GO:0000786 GO:0000786 nucleosome
## GO:1902554 GO:1902554 serine/threonine protein kinase complex
## GO:1902911 GO:1902911 protein kinase complex
## GeneRatio BgRatio pvalue p.adjust qvalue geneID
## GO:0070557 1/3 2/19894 0.0003015833 0.003015833 0.0009523684 CDKN1A
## GO:0000307 1/3 56/19894 0.0084214303 0.042107152 0.0132969953 CDKN1A
## GO:0000786 1/3 135/19894 0.0202210709 0.044901762 0.0141795038 TGM2
## GO:1902554 1/3 136/19894 0.0203698303 0.044901762 0.0141795038 CDKN1A
## GO:1902911 1/3 150/19894 0.0224508810 0.044901762 0.0141795038 CDKN1A
## Count
## GO:0070557 1
## GO:0000307 1
## GO:0000786 1
## GO:1902554 1
## GO:1902911 1
## ID Description GeneRatio
## GO:0120283 GO:0120283 protein serine/threonine kinase binding 2/17
## GO:0005178 GO:0005178 integrin binding 3/17
## GO:0043394 GO:0043394 proteoglycan binding 2/17
## GO:0003925 GO:0003925 G protein activity 2/17
## GO:0030374 GO:0030374 nuclear receptor coactivator activity 2/17
## GO:0005518 GO:0005518 collagen binding 2/17
## BgRatio pvalue p.adjust qvalue geneID Count
## GO:0120283 7/18522 1.660593e-05 0.002391254 0.001013836 XIAP/MAPK8 2
## GO:0005178 157/18522 3.723281e-04 0.022018344 0.009335263 PTK2/ITGA2/FN1 3
## GO:0043394 36/18522 4.904396e-04 0.022018344 0.009335263 ITGA2/FN1 2
## GO:0003925 45/18522 7.669576e-04 0.022018344 0.009335263 KRAS/NRAS 2
## GO:0030374 55/18522 1.144248e-03 0.022018344 0.009335263 ETS1/NCOA3 2
## GO:0005518 68/18522 1.743022e-03 0.022018344 0.009335263 ITGA2/FN1 2
## ID Description
## GO:0051402 GO:0051402 neuron apoptotic process
## GO:2000045 GO:2000045 regulation of G1/S transition of mitotic cell cycle
## GO:1902806 GO:1902806 regulation of cell cycle G1/S phase transition
## GO:0007044 GO:0007044 cell-substrate junction assembly
## GO:0000082 GO:0000082 G1/S transition of mitotic cell cycle
## GO:0150115 GO:0150115 cell-substrate junction organization
## GeneRatio BgRatio pvalue p.adjust qvalue
## GO:0051402 6/17 292/18888 1.390911e-07 0.0001708038 8.784699e-05
## GO:2000045 5/17 185/18888 4.803076e-07 0.0002949089 1.516761e-04
## GO:1902806 5/17 211/18888 9.204379e-07 0.0003763699 1.935727e-04
## GO:0007044 4/17 96/18888 1.417572e-06 0.0003763699 1.935727e-04
## GO:0000082 5/17 234/18888 1.532451e-06 0.0003763699 1.935727e-04
## GO:0150115 4/17 103/18888 1.879404e-06 0.0003846513 1.978320e-04
## geneID Count
## GO:0051402 XIAP/BID/KRAS/ATM/CCND1/G6PD 6
## GO:2000045 ARID1A/BID/PTEN/ATM/CCND1 5
## GO:1902806 ARID1A/BID/PTEN/ATM/CCND1 5
## GO:0007044 PTEN/PTK2/ITGA2/FN1 4
## GO:0000082 ARID1A/BID/PTEN/ATM/CCND1 5
## GO:0150115 PTEN/PTK2/ITGA2/FN1 4
## ID Description GeneRatio BgRatio
## GO:0009898 GO:0009898 cytoplasmic side of plasma membrane 3/17 161/19894
## GO:0098562 GO:0098562 cytoplasmic side of membrane 3/17 199/19894
## GO:0097128 GO:0097128 cyclin D1-CDK4 complex 1/17 2/19894
## GO:0034666 GO:0034666 integrin alpha2-beta1 complex 1/17 3/19894
## GO:0016324 GO:0016324 apical plasma membrane 3/17 402/19894
## GO:0035749 GO:0035749 myelin sheath adaxonal region 1/17 6/19894
## pvalue p.adjust qvalue geneID Count
## GO:0009898 0.0003254665 0.02387945 0.01559085 PTEN/KRAS/G6PD 3
## GO:0098562 0.0006045430 0.02387945 0.01559085 PTEN/KRAS/G6PD 3
## GO:0097128 0.0017083707 0.04498710 0.02937199 CCND1 1
## GO:0034666 0.0025615256 0.04808042 0.03139161 ITGA2 1
## GO:0016324 0.0045109740 0.04808042 0.03139161 PTEN/IGFBP2/FN1 3
## GO:0035749 0.0051168749 0.04808042 0.03139161 PTEN 1
## ID
## GO:0140297 GO:0140297
## GO:0097718 GO:0097718
## GO:0061629 GO:0061629
## GO:0120283 GO:0120283
## GO:0003713 GO:0003713
## GO:0031625 GO:0031625
## Description
## GO:0140297 DNA-binding transcription factor binding
## GO:0097718 disordered domain specific binding
## GO:0061629 RNA polymerase II-specific DNA-binding transcription factor binding
## GO:0120283 protein serine/threonine kinase binding
## GO:0003713 transcription coactivator activity
## GO:0031625 ubiquitin protein ligase binding
## GeneRatio BgRatio pvalue p.adjust qvalue
## GO:0140297 6/13 478/18522 4.212624e-07 4.844518e-05 1.818080e-05
## GO:0097718 3/13 32/18522 1.324045e-06 7.613260e-05 2.857150e-05
## GO:0061629 5/13 343/18522 2.409607e-06 9.236828e-05 3.466453e-05
## GO:0120283 2/13 7/18522 9.530849e-06 2.740119e-04 1.028328e-04
## GO:0003713 4/13 271/18522 2.888346e-05 6.643195e-04 2.493099e-04
## GO:0031625 4/13 305/18522 4.584195e-05 8.786374e-04 3.297404e-04
## geneID Count
## GO:0140297 RB1/ETS1/ARID1A/YWHAZ/NCOA3/CTNNB1 6
## GO:0097718 RB1/NCOA3/CTNNB1 3
## GO:0061629 RB1/ETS1/ARID1A/NCOA3/CTNNB1 5
## GO:0120283 XIAP/MAPK8 2
## GO:0003713 ETS1/ARID1A/NCOA3/CTNNB1 4
## GO:0031625 RB1/BID/YWHAZ/CTNNB1 4
## ID Description
## GO:0051402 GO:0051402 neuron apoptotic process
## GO:2000045 GO:2000045 regulation of G1/S transition of mitotic cell cycle
## GO:0030099 GO:0030099 myeloid cell differentiation
## GO:1902806 GO:1902806 regulation of cell cycle G1/S phase transition
## GO:0000082 GO:0000082 G1/S transition of mitotic cell cycle
## GO:0002573 GO:0002573 myeloid leukocyte differentiation
## GeneRatio BgRatio pvalue p.adjust qvalue
## GO:0051402 5/13 292/18888 9.922177e-07 0.001120214 0.0004783534
## GO:2000045 4/13 185/18888 5.945103e-06 0.002752834 0.0011755143
## GO:0030099 5/13 439/18888 7.314882e-06 0.002752834 0.0011755143
## GO:1902806 4/13 211/18888 1.000067e-05 0.002822690 0.0012053442
## GO:0000082 4/13 234/18888 1.503686e-05 0.003074891 0.0013130390
## GO:0002573 4/13 239/18888 1.634132e-05 0.003074891 0.0013130390
## geneID Count
## GO:0051402 RB1/XIAP/BID/CTNNB1/CCND1 5
## GO:2000045 RB1/ARID1A/BID/CCND1 4
## GO:0030099 RB1/ETS1/GAB2/CTNNB1/FASN 5
## GO:1902806 RB1/ARID1A/BID/CCND1 4
## GO:0000082 RB1/ARID1A/BID/CCND1 4
## GO:0002573 RB1/GAB2/CTNNB1/FASN 4
## ID Description
## GO:0016514 GO:0016514 SWI/SNF complex
## GO:0000307 GO:0000307 cyclin-dependent protein kinase holoenzyme complex
## GO:0017053 GO:0017053 transcription repressor complex
## GO:0034750 GO:0034750 Scrib-APC-beta-catenin complex
## GO:0097128 GO:0097128 cyclin D1-CDK4 complex
## GO:1990711 GO:1990711 beta-catenin-ICAT complex
## GeneRatio BgRatio pvalue p.adjust qvalue geneID
## GO:0016514 2/13 30/19894 0.0001697103 0.01764987 0.007860266 RB1/ARID1A
## GO:0000307 2/13 56/19894 0.0005950830 0.01971858 0.008781556 RB1/CCND1
## GO:0017053 2/13 77/19894 0.0011219415 0.01971858 0.008781556 CTNNB1/CCND1
## GO:0034750 1/13 2/19894 0.0013065325 0.01971858 0.008781556 CTNNB1
## GO:0097128 1/13 2/19894 0.0013065325 0.01971858 0.008781556 CCND1
## GO:1990711 1/13 2/19894 0.0013065325 0.01971858 0.008781556 CTNNB1
## Count
## GO:0016514 2
## GO:0000307 2
## GO:0017053 2
## GO:0034750 1
## GO:0097128 1
## GO:1990711 1
## ID Description GeneRatio
## GO:0005178 GO:0005178 integrin binding 4/25
## GO:0106310 GO:0106310 protein serine kinase activity 5/25
## GO:0004707 GO:0004707 MAP kinase activity 2/25
## GO:0004674 GO:0004674 protein serine/threonine kinase activity 5/25
## GO:0070064 GO:0070064 proline-rich region binding 2/25
## GO:0042826 GO:0042826 histone deacetylase binding 3/25
## BgRatio pvalue p.adjust qvalue
## GO:0005178 157/18522 5.470368e-05 0.008786504 0.003808392
## GO:0106310 363/18522 1.081824e-04 0.008786504 0.003808392
## GO:0004707 16/18522 2.074657e-04 0.008786504 0.003808392
## GO:0004674 427/18522 2.308630e-04 0.008786504 0.003808392
## GO:0070064 17/18522 2.349333e-04 0.008786504 0.003808392
## GO:0042826 128/18522 6.634074e-04 0.020676198 0.008961819
## geneID Count
## GO:0005178 MYH9/PTK2/ITGA2/FN1 4
## GO:0106310 AKT1/MTOR/MAPK8/ATM/MAPK1 5
## GO:0004707 MAPK8/MAPK1 2
## GO:0004674 AKT1/MTOR/MAPK8/ATM/MAPK1 5
## GO:0070064 CCND1/YAP1 2
## GO:0042826 HSPA1A/MAPK8/CCND1 3
## ID Description GeneRatio BgRatio
## GO:0001667 GO:0001667 ameboidal-type cell migration 10/25 498/18888
## GO:0010631 GO:0010631 epithelial cell migration 9/25 375/18888
## GO:0090132 GO:0090132 epithelium migration 9/25 378/18888
## GO:0090130 GO:0090130 tissue migration 9/25 383/18888
## GO:0062197 GO:0062197 cellular response to chemical stress 8/25 311/18888
## GO:0071214 GO:0071214 cellular response to abiotic stimulus 8/25 334/18888
## pvalue p.adjust qvalue
## GO:0001667 3.401019e-10 4.073661e-07 1.676456e-07
## GO:0010631 6.722030e-10 4.073661e-07 1.676456e-07
## GO:0090132 7.210613e-10 4.073661e-07 1.676456e-07
## GO:0090130 8.094706e-10 4.073661e-07 1.676456e-07
## GO:0062197 4.187089e-09 1.685722e-06 6.937345e-07
## GO:0071214 7.318853e-09 2.104693e-06 8.661560e-07
## geneID Count
## GO:0001667 AKT1/MTOR/MYH9/PTEN/PTK2/ETS1/STAT5A/ITGA2/ANLN/FN1 10
## GO:0010631 AKT1/MTOR/MYH9/PTEN/PTK2/ETS1/STAT5A/ITGA2/ANLN 9
## GO:0090132 AKT1/MTOR/MYH9/PTEN/PTK2/ETS1/STAT5A/ITGA2/ANLN 9
## GO:0090130 AKT1/MTOR/MYH9/PTEN/PTK2/ETS1/STAT5A/ITGA2/ANLN 9
## GO:0062197 HSPA1A/AKT1/MTOR/MAPK8/FOXO3/ATM/MAPK1/G6PD 8
## GO:0071214 MTOR/MAPK8/CDKN1A/ATM/CASP8/PTEN/YAP1/ITGA2 8
## ID Description GeneRatio BgRatio
## GO:0005925 GO:0005925 focal adhesion 7/25 421/19894
## GO:0030055 GO:0030055 cell-substrate junction 7/25 431/19894
## GO:0005826 GO:0005826 actomyosin contractile ring 2/25 4/19894
## GO:0009898 GO:0009898 cytoplasmic side of plasma membrane 4/25 161/19894
## GO:0070938 GO:0070938 contractile ring 2/25 10/19894
## GO:0098562 GO:0098562 cytoplasmic side of membrane 4/25 199/19894
## pvalue p.adjust qvalue
## GO:0005925 6.252929e-07 0.0000483075 2.735114e-05
## GO:0030055 7.319319e-07 0.0000483075 2.735114e-05
## GO:0005826 9.082603e-06 0.0003996345 2.262684e-04
## GO:0009898 4.578147e-05 0.0015107886 8.553907e-04
## GO:0070938 6.780516e-05 0.0017900563 1.013509e-03
## GO:0098562 1.042248e-04 0.0022929450 1.298238e-03
## geneID Count
## GO:0005925 HSPA1A/MYH9/KRAS/PTK2/ITGA2/MAPK1/TGM2 7
## GO:0030055 HSPA1A/MYH9/KRAS/PTK2/ITGA2/MAPK1/TGM2 7
## GO:0005826 MYH9/ANLN 2
## GO:0009898 MYH9/PTEN/KRAS/G6PD 4
## GO:0070938 MYH9/ANLN 2
## GO:0098562 MYH9/PTEN/KRAS/G6PD 4
## ID
## GO:0140297 GO:0140297
## GO:0001221 GO:0001221
## GO:0019902 GO:0019902
## GO:0016538 GO:0016538
## GO:0019887 GO:0019887
## GO:0106310 GO:0106310
## Description
## GO:0140297 DNA-binding transcription factor binding
## GO:0001221 transcription coregulator binding
## GO:0019902 phosphatase binding
## GO:0016538 cyclin-dependent protein serine/threonine kinase regulator activity
## GO:0019887 protein kinase regulator activity
## GO:0106310 protein serine kinase activity
## GeneRatio BgRatio pvalue p.adjust qvalue
## GO:0140297 10/42 478/18522 8.369349e-08 2.402003e-05 1.030751e-05
## GO:0001221 6/42 114/18522 2.084959e-07 2.991917e-05 1.283896e-05
## GO:0019902 6/42 189/18522 4.029967e-06 3.498304e-04 1.501198e-04
## GO:0016538 4/42 50/18522 4.875685e-06 3.498304e-04 1.501198e-04
## GO:0019887 6/42 232/18522 1.302402e-05 6.850613e-04 2.939746e-04
## GO:0106310 7/42 363/18522 1.566342e-05 6.850613e-04 2.939746e-04
## geneID Count
## GO:0140297 ESR1/BCL2/VHL/ETS1/PARP1/STAT5A/MYC/YAP1/CTNNB1/GATA3 10
## GO:0001221 ESR1/FOXO3/ETS1/MYC/CTNNB1/GATA3 6
## GO:0019902 MET/BCL2/MAPK8/PTK2/MAPK1/CTNNB1 6
## GO:0016538 CCND1/CDKN1A/CCNE2/CASP3 4
## GO:0019887 CCND1/AKT1/CDKN1A/CCNE2/CASP3/PIK3CA 6
## GO:0106310 AKT1/MTOR/MAPK8/ATM/CHEK1/PIK3CA/MAPK1 7
## ID Description GeneRatio
## GO:0071214 GO:0071214 cellular response to abiotic stimulus 15/42
## GO:0104004 GO:0104004 cellular response to environmental stimulus 15/42
## GO:0043523 GO:0043523 regulation of neuron apoptotic process 13/42
## GO:0048732 GO:0048732 gland development 15/42
## GO:0051402 GO:0051402 neuron apoptotic process 13/42
## GO:0010631 GO:0010631 epithelial cell migration 13/42
## BgRatio pvalue p.adjust qvalue
## GO:0071214 334/18888 2.422177e-16 3.542434e-13 1.393389e-13
## GO:0104004 334/18888 2.422177e-16 3.542434e-13 1.393389e-13
## GO:0043523 244/18888 3.707763e-15 3.615069e-12 1.421960e-12
## GO:0048732 449/18888 1.902889e-14 1.391488e-11 5.473310e-12
## GO:0051402 292/18888 3.771394e-14 2.206265e-11 8.678175e-12
## GO:0010631 375/18888 9.185809e-13 4.245967e-10 1.670118e-10
## geneID
## GO:0071214 IGF1R/MTOR/MAPK8/CDKN1A/ATM/CASP8/PTEN/PARP1/MYC/CASP3/YAP1/CHEK1/ITGA2/PIK3CA/GATA3
## GO:0104004 IGF1R/MTOR/MAPK8/CDKN1A/ATM/CASP8/PTEN/PARP1/MYC/CASP3/YAP1/CHEK1/ITGA2/PIK3CA/GATA3
## GO:0043523 G6PD/BCL2/KRAS/CCND1/FOXO3/ATM/CASP8/PARP1/CASP3/BCL2L11/PIK3CA/CTNNB1/GATA3
## GO:0048732 ESR1/MET/BCL2/CCND1/AKT1/ATM/STAT5A/BCL2L11/ITGA2/PIK3CA/MAPK1/SRSF1/CTNNB1/TGM2/GATA3
## GO:0051402 G6PD/BCL2/KRAS/CCND1/FOXO3/ATM/CASP8/PARP1/CASP3/BCL2L11/PIK3CA/CTNNB1/GATA3
## GO:0010631 MET/AKT1/MTOR/MYH9/PTEN/PTK2/ETS1/RAB25/STAT5A/ITGA2/PIK3CA/ANLN/GATA3
## Count
## GO:0071214 15
## GO:0104004 15
## GO:0043523 13
## GO:0048732 15
## GO:0051402 13
## GO:0010631 13
## ID Description
## GO:0005925 GO:0005925 focal adhesion
## GO:0030055 GO:0030055 cell-substrate junction
## GO:0090571 GO:0090571 RNA polymerase II transcription repressor complex
## GO:0005741 GO:0005741 mitochondrial outer membrane
## GO:0031968 GO:0031968 organelle outer membrane
## GO:0019867 GO:0019867 outer membrane
## GeneRatio BgRatio pvalue p.adjust qvalue
## GO:0005925 8/42 421/19894 2.364807e-06 0.0002594590 0.0001413609
## GO:0030055 8/42 431/19894 2.814238e-06 0.0002594590 0.0001413609
## GO:0090571 3/42 15/19894 3.911442e-06 0.0002594590 0.0001413609
## GO:0005741 6/42 219/19894 6.261413e-06 0.0003115053 0.0001697172
## GO:0031968 6/42 248/19894 1.272480e-05 0.0004417170 0.0002406604
## GO:0019867 6/42 250/19894 1.331810e-05 0.0004417170 0.0002406604
## geneID Count
## GO:0005925 KRAS/HSPA1A/MYH9/PTK2/ITGA2/MAPK1/CTNNB1/TGM2 8
## GO:0030055 KRAS/HSPA1A/MYH9/PTK2/ITGA2/MAPK1/CTNNB1/TGM2 8
## GO:0090571 FOXO3/MYC/CTNNB1 3
## GO:0005741 BCL2/KRAS/MTOR/FOXO3/CASP8/BCL2L11 6
## GO:0031968 BCL2/KRAS/MTOR/FOXO3/CASP8/BCL2L11 6
## GO:0019867 BCL2/KRAS/MTOR/FOXO3/CASP8/BCL2L11 6
## ID
## GO:0120283 GO:0120283
## GO:0003713 GO:0003713
## GO:0030374 GO:0030374
## GO:0061629 GO:0061629
## GO:0016410 GO:0016410
## GO:0140297 GO:0140297
## Description
## GO:0120283 protein serine/threonine kinase binding
## GO:0003713 transcription coactivator activity
## GO:0030374 nuclear receptor coactivator activity
## GO:0061629 RNA polymerase II-specific DNA-binding transcription factor binding
## GO:0016410 N-acyltransferase activity
## GO:0140297 DNA-binding transcription factor binding
## GeneRatio BgRatio pvalue p.adjust qvalue
## GO:0120283 2/8 7/18522 3.424411e-06 0.000232860 9.732538e-05
## GO:0003713 3/8 271/18522 1.642917e-04 0.005432205 2.270426e-03
## GO:0030374 2/8 55/18522 2.396561e-04 0.005432205 2.270426e-03
## GO:0061629 3/8 343/18522 3.290146e-04 0.005593248 2.337735e-03
## GO:0016410 2/8 95/18522 7.143770e-04 0.009715527 4.060669e-03
## GO:0140297 3/8 478/18522 8.683135e-04 0.009840887 4.113064e-03
## geneID Count
## GO:0120283 XIAP/MAPK8 2
## GO:0003713 ETS1/ARID1A/NCOA3 3
## GO:0030374 ETS1/NCOA3 2
## GO:0061629 ETS1/ARID1A/NCOA3 3
## GO:0016410 NCOA3/TGM2 2
## GO:0140297 ETS1/ARID1A/NCOA3 3
## ID Description
## GO:1902459 GO:1902459 positive regulation of stem cell population maintenance
## GO:0030522 GO:0030522 intracellular receptor signaling pathway
## GO:2000036 GO:2000036 regulation of stem cell population maintenance
## GO:0018277 GO:0018277 protein deamination
## GO:1902528 GO:1902528 regulation of protein linear polyubiquitination
## GO:1902530 GO:1902530 positive regulation of protein linear polyubiquitination
## GeneRatio BgRatio pvalue p.adjust qvalue
## GO:1902459 2/8 48/18888 0.0001753538 0.04414629 0.02178271
## GO:0030522 3/8 369/18888 0.0003850393 0.04414629 0.02178271
## GO:2000036 2/8 73/18888 0.0004063778 0.04414629 0.02178271
## GO:0018277 1/8 2/18888 0.0008469417 0.04414629 0.02178271
## GO:1902528 1/8 2/18888 0.0008469417 0.04414629 0.02178271
## GO:1902530 1/8 2/18888 0.0008469417 0.04414629 0.02178271
## geneID Count
## GO:1902459 ARID1A/NCOA3 2
## GO:0030522 XIAP/MAPK8/ARID1A 3
## GO:2000036 ARID1A/NCOA3 2
## GO:0018277 TGM2 1
## GO:1902528 XIAP 1
## GO:1902530 XIAP 1
## ID Description GeneRatio BgRatio pvalue p.adjust
## GO:0097441 GO:0097441 basal dendrite 1/8 6/19894 0.002410666 0.02181829
## GO:0140092 GO:0140092 bBAF complex 1/8 10/19894 0.004014950 0.02181829
## GO:0035060 GO:0035060 brahma complex 1/8 14/19894 0.005616977 0.02181829
## GO:0071564 GO:0071564 npBAF complex 1/8 14/19894 0.005616977 0.02181829
## GO:0071565 GO:0071565 nBAF complex 1/8 16/19894 0.006417144 0.02181829
## GO:0016514 GO:0016514 SWI/SNF complex 1/8 30/19894 0.012002558 0.03400725
## qvalue geneID Count
## GO:0097441 0.01350978 MAPK8 1
## GO:0140092 0.01350978 ARID1A 1
## GO:0035060 0.01350978 ARID1A 1
## GO:0071564 0.01350978 ARID1A 1
## GO:0071565 0.01350978 ARID1A 1
## GO:0016514 0.02105712 ARID1A 1
## ID
## GO:0004345 GO:0004345
## GO:0005536 GO:0005536
## GO:0050661 GO:0050661
## GO:0048029 GO:0048029
## GO:0016616 GO:0016616
## GO:0016614 GO:0016614
## Description
## GO:0004345 glucose-6-phosphate dehydrogenase activity
## GO:0005536 glucose binding
## GO:0050661 NADP binding
## GO:0048029 monosaccharide binding
## GO:0016616 oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
## GO:0016614 oxidoreductase activity, acting on CH-OH group of donors
## GeneRatio BgRatio pvalue p.adjust qvalue geneID Count
## GO:0004345 1/1 2/18522 0.0001079797 0.0007558579 NA G6PD 1
## GO:0005536 1/1 11/18522 0.0005938883 0.0020786092 NA G6PD 1
## GO:0050661 1/1 53/18522 0.0028614620 0.0066767448 NA G6PD 1
## GO:0048029 1/1 74/18522 0.0039952489 0.0069916856 NA G6PD 1
## GO:0016616 1/1 125/18522 0.0067487312 0.0085034014 NA G6PD 1
## GO:0016614 1/1 135/18522 0.0072886297 0.0085034014 NA G6PD 1
## ID
## GO:0010731 GO:0010731
## GO:0010732 GO:0010732
## GO:0010734 GO:0010734
## GO:0019322 GO:0019322
## GO:1904879 GO:1904879
## GO:0009051 GO:0009051
## Description
## GO:0010731 protein glutathionylation
## GO:0010732 regulation of protein glutathionylation
## GO:0010734 negative regulation of protein glutathionylation
## GO:0019322 pentose biosynthetic process
## GO:1904879 positive regulation of calcium ion transmembrane transport via high voltage-gated calcium channel
## GO:0009051 pentose-phosphate shunt, oxidative branch
## GeneRatio BgRatio pvalue p.adjust qvalue geneID Count
## GO:0010731 1/1 2/18888 0.0001058873 0.003388395 NA G6PD 1
## GO:0010732 1/1 2/18888 0.0001058873 0.003388395 NA G6PD 1
## GO:0010734 1/1 2/18888 0.0001058873 0.003388395 NA G6PD 1
## GO:0019322 1/1 2/18888 0.0001058873 0.003388395 NA G6PD 1
## GO:1904879 1/1 3/18888 0.0001588310 0.003872451 NA G6PD 1
## GO:0009051 1/1 4/18888 0.0002117747 0.003872451 NA G6PD 1
## ID Description GeneRatio BgRatio
## GO:0034451 GO:0034451 centriolar satellite 1/1 126/19894
## GO:0009898 GO:0009898 cytoplasmic side of plasma membrane 1/1 161/19894
## GO:0098562 GO:0098562 cytoplasmic side of membrane 1/1 199/19894
## pvalue p.adjust qvalue geneID Count
## GO:0034451 0.006333568 0.01000302 NA G6PD 1
## GO:0009898 0.008092892 0.01000302 NA G6PD 1
## GO:0098562 0.010003016 0.01000302 NA G6PD 1
## NULL
## NULL
## NULL
## ID Description GeneRatio BgRatio
## GO:0043559 GO:0043559 insulin binding 2/8 5/18522
## GO:0043560 GO:0043560 insulin receptor substrate binding 2/8 13/18522
## GO:0005158 GO:0005158 insulin receptor binding 2/8 22/18522
## GO:0043548 GO:0043548 phosphatidylinositol 3-kinase binding 2/8 25/18522
## GO:0017046 GO:0017046 peptide hormone binding 2/8 50/18522
## GO:0033218 GO:0033218 amide binding 3/8 409/18522
## pvalue p.adjust qvalue geneID Count
## GO:0043559 1.631377e-06 0.0001761887 6.182059e-05 PIK3R1/IGF1R 2
## GO:0043560 1.270277e-05 0.0006859494 2.406840e-04 PIK3R1/IGF1R 2
## GO:0005158 3.754665e-05 0.0013157179 4.616554e-04 PIK3R1/IGF1R 2
## GO:0043548 4.873029e-05 0.0013157179 4.616554e-04 PIK3R1/IGF1R 2
## GO:0017046 1.979099e-04 0.0042748535 1.499949e-03 PIK3R1/IGF1R 2
## GO:0033218 5.511240e-04 0.0049093069 1.722564e-03 PIK3R1/IGF1R/FASN 3
## ID Description
## GO:0031099 GO:0031099 regeneration
## GO:0097421 GO:0097421 liver regeneration
## GO:0071353 GO:0071353 cellular response to interleukin-4
## GO:0070670 GO:0070670 response to interleukin-4
## GO:0033120 GO:0033120 positive regulation of RNA splicing
## GO:0048009 GO:0048009 insulin-like growth factor receptor signaling pathway
## GeneRatio BgRatio pvalue p.adjust qvalue
## GO:0031099 3/8 200/18888 6.298081e-05 0.01533276 0.006745377
## GO:0097421 2/8 30/18888 6.788160e-05 0.01533276 0.006745377
## GO:0071353 2/8 34/18888 8.746969e-05 0.01533276 0.006745377
## GO:0070670 2/8 37/18888 1.037750e-04 0.01533276 0.006745377
## GO:0033120 2/8 50/18888 1.903523e-04 0.01886635 0.008299917
## GO:0048009 2/8 53/18888 2.139908e-04 0.01886635 0.008299917
## geneID Count
## GO:0031099 CCND1/IGF1R/SRSF1 3
## GO:0097421 CCND1/SRSF1 2
## GO:0071353 TUBA1B/FASN 2
## GO:0070670 TUBA1B/FASN 2
## GO:0033120 PIK3R1/SRSF1 2
## GO:0048009 PIK3R1/IGF1R 2
## ID
## GO:0061695 GO:0061695
## GO:0097128 GO:0097128
## GO:1902911 GO:1902911
## GO:0005899 GO:0005899
## GO:0035867 GO:0035867
## GO:1990578 GO:1990578
## Description
## GO:0061695 transferase complex, transferring phosphorus-containing groups
## GO:0097128 cyclin D1-CDK4 complex
## GO:1902911 protein kinase complex
## GO:0005899 insulin receptor complex
## GO:0035867 alphav-beta3 integrin-IGF-1-IGF1R complex
## GO:1990578 perinuclear endoplasmic reticulum membrane
## GeneRatio BgRatio pvalue p.adjust qvalue
## GO:0061695 3/8 308/19894 0.0001942755 0.008353845 0.003681009
## GO:0097128 1/8 2/19894 0.0008041211 0.011521680 0.005076873
## GO:1902911 2/8 150/19894 0.0015348825 0.011521680 0.005076873
## GO:0005899 1/8 4/19894 0.0016076763 0.011521680 0.005076873
## GO:0035867 1/8 4/19894 0.0016076763 0.011521680 0.005076873
## GO:1990578 1/8 4/19894 0.0016076763 0.011521680 0.005076873
## geneID Count
## GO:0061695 CCND1/PIK3R1/IGF1R 3
## GO:0097128 CCND1 1
## GO:1902911 CCND1/IGF1R 2
## GO:0005899 IGF1R 1
## GO:0035867 IGF1R 1
## GO:1990578 PIK3R1 1
## ID Description GeneRatio BgRatio
## GO:0019903 GO:0019903 protein phosphatase binding 9/57 142/18522
## GO:0019902 GO:0019902 phosphatase binding 9/57 189/18522
## GO:0140313 GO:0140313 molecular sequestering activity 6/57 49/18522
## GO:0031625 GO:0031625 ubiquitin protein ligase binding 10/57 305/18522
## GO:0044389 GO:0044389 ubiquitin-like protein ligase binding 10/57 324/18522
## GO:0001221 GO:0001221 transcription coregulator binding 7/57 114/18522
## pvalue p.adjust qvalue
## GO:0019903 4.664299e-10 1.641833e-07 7.610172e-08
## GO:0019902 5.845927e-09 9.599120e-07 4.449353e-07
## GO:0140313 8.181068e-09 9.599120e-07 4.449353e-07
## GO:0031625 2.756780e-08 2.425967e-06 1.124476e-06
## GO:0044389 4.869142e-08 3.342587e-06 1.549345e-06
## GO:0001221 5.697591e-08 3.342587e-06 1.549345e-06
## geneID Count
## GO:0019903 MET/BCL2/CDKN1B/MAPK8/PTK2/MAPT/EGFR/STAT3/CTNNB1 9
## GO:0019902 MET/BCL2/CDKN1B/MAPK8/PTK2/MAPT/EGFR/STAT3/CTNNB1 9
## GO:0140313 YWHAZ/CDKN1A/CAV1/STAT3/SQSTM1/LCN2 6
## GO:0031625 BCL2/CDKN1B/JUN/BID/YWHAZ/CHEK2/CDKN1A/EGFR/SQSTM1/CTNNB1 10
## GO:0044389 BCL2/CDKN1B/JUN/BID/YWHAZ/CHEK2/CDKN1A/EGFR/SQSTM1/CTNNB1 10
## GO:0001221 ESR1/MYC/EZH2/ETS1/FOXO3/GATA3/CTNNB1 7
## ID Description
## GO:0032355 GO:0032355 response to estradiol
## GO:0000082 GO:0000082 G1/S transition of mitotic cell cycle
## GO:2000045 GO:2000045 regulation of G1/S transition of mitotic cell cycle
## GO:0044772 GO:0044772 mitotic cell cycle phase transition
## GO:0048872 GO:0048872 homeostasis of number of cells
## GO:0044843 GO:0044843 cell cycle G1/S phase transition
## GeneRatio BgRatio pvalue p.adjust qvalue
## GO:0032355 12/57 115/18888 8.100857e-16 2.599565e-12 1.182725e-12
## GO:0000082 14/57 234/18888 6.519083e-15 8.973148e-12 4.082517e-12
## GO:2000045 13/57 185/18888 8.388733e-15 8.973148e-12 4.082517e-12
## GO:0044772 17/57 451/18888 1.148367e-14 9.212771e-12 4.191538e-12
## GO:0048872 15/57 322/18888 2.494598e-14 1.601033e-11 7.284227e-12
## GO:0044843 14/57 262/18888 3.118815e-14 1.668046e-11 7.589117e-12
## geneID
## GO:0032355 ESR1/ERRFI1/IGF1R/CDKN1B/EZH2/NCOA3/EGFR/CASP3/STAT3/IGFBP2/ITGA2/CTNNB1
## GO:0000082 BCL2/CCND1/AKT1/PTEN/CDKN1B/MYC/EZH2/ARID1A/BID/ATM/CHEK2/CDKN1A/EGFR/CCNE2
## GO:2000045 BCL2/CCND1/AKT1/PTEN/CDKN1B/EZH2/ARID1A/BID/ATM/CHEK2/CDKN1A/EGFR/CCNE2
## GO:0044772 BCL2/CCND1/AKT1/PTEN/CDKN1B/MYC/EZH2/ARID1A/BID/ATM/CHEK2/CDKN1A/EGFR/CHEK1/FOXM1/CCNE2/RAD50
## GO:0048872 BAP1/G6PD/BCL2/KRAS/AKT1/BCL2L11/EZH2/XIAP/ETS1/AXL/CASP3/ANXA1/FOXO3/STAT3/GATA3
## GO:0044843 BCL2/CCND1/AKT1/PTEN/CDKN1B/MYC/EZH2/ARID1A/BID/ATM/CHEK2/CDKN1A/EGFR/CCNE2
## Count
## GO:0032355 12
## GO:0000082 14
## GO:2000045 13
## GO:0044772 17
## GO:0048872 15
## GO:0044843 14
## ID Description
## GO:0005925 GO:0005925 focal adhesion
## GO:0030055 GO:0030055 cell-substrate junction
## GO:0070435 GO:0070435 Shc-EGFR complex
## GO:0090571 GO:0090571 RNA polymerase II transcription repressor complex
## GO:0045121 GO:0045121 membrane raft
## GO:0098857 GO:0098857 membrane microdomain
## GeneRatio BgRatio pvalue p.adjust qvalue
## GO:0005925 9/57 421/19894 2.861306e-06 0.0003863119 0.0002388806
## GO:0030055 9/57 431/19894 3.464681e-06 0.0003863119 0.0002388806
## GO:0070435 2/57 2/19894 8.065671e-06 0.0005520325 0.0003413559
## GO:0090571 3/57 15/19894 9.901927e-06 0.0005520325 0.0003413559
## GO:0045121 7/57 286/19894 1.686241e-05 0.0006409717 0.0003963526
## GO:0098857 7/57 287/19894 1.724587e-05 0.0006409717 0.0003963526
## geneID Count
## GO:0005925 KRAS/SHC1/PTK2/YWHAZ/EGFR/CAV1/ANXA1/ITGA2/CTNNB1 9
## GO:0030055 KRAS/SHC1/PTK2/YWHAZ/EGFR/CAV1/ANXA1/ITGA2/CTNNB1 9
## GO:0070435 SHC1/EGFR 2
## GO:0090571 MYC/FOXO3/CTNNB1 3
## GO:0045121 IGF1R/IRS1/MAPT/EGFR/CAV1/GAB2/CTNNB1 7
## GO:0098857 IGF1R/IRS1/MAPT/EGFR/CAV1/GAB2/CTNNB1 7
## ID Description GeneRatio
## GO:0019902 GO:0019902 phosphatase binding 5/32
## GO:0106310 GO:0106310 protein serine kinase activity 6/32
## GO:0030235 GO:0030235 nitric-oxide synthase regulator activity 2/32
## GO:0004674 GO:0004674 protein serine/threonine kinase activity 6/32
## GO:0019903 GO:0019903 protein phosphatase binding 4/32
## GO:0140297 GO:0140297 DNA-binding transcription factor binding 6/32
## BgRatio pvalue p.adjust qvalue
## GO:0019902 189/18522 1.689255e-05 0.003714311 0.001533586
## GO:0106310 363/18522 3.201993e-05 0.003714311 0.001533586
## GO:0030235 7/18522 6.039943e-05 0.004580884 0.001891382
## GO:0004674 427/18522 7.898077e-05 0.004580884 0.001891382
## GO:0019903 142/18522 1.007745e-04 0.004675937 0.001930627
## GO:0140297 478/18522 1.466379e-04 0.004750490 0.001961409
## geneID Count
## GO:0019902 MET/BCL2/MAPK8/PTK2/MAPK1 5
## GO:0106310 AKT1/MTOR/MAPK8/ATM/CHEK1/MAPK1 6
## GO:0030235 ESR1/AKT1 2
## GO:0004674 AKT1/MTOR/MAPK8/ATM/CHEK1/MAPK1 6
## GO:0019903 MET/BCL2/MAPK8/PTK2 4
## GO:0140297 ESR1/BCL2/VHL/ETS1/STAT5A/YAP1 6
## ID Description GeneRatio
## GO:0071214 GO:0071214 cellular response to abiotic stimulus 10/32
## GO:0104004 GO:0104004 cellular response to environmental stimulus 10/32
## GO:0071496 GO:0071496 cellular response to external stimulus 10/32
## GO:0001667 GO:0001667 ameboidal-type cell migration 11/32
## GO:0010631 GO:0010631 epithelial cell migration 10/32
## GO:0090132 GO:0090132 epithelium migration 10/32
## BgRatio pvalue p.adjust qvalue
## GO:0071214 334/18888 1.194244e-10 9.640605e-08 3.973773e-08
## GO:0104004 334/18888 1.194244e-10 9.640605e-08 3.973773e-08
## GO:0071496 335/18888 1.229669e-10 9.640605e-08 3.973773e-08
## GO:0001667 498/18888 2.999935e-10 1.523023e-07 6.277768e-08
## GO:0010631 375/18888 3.692513e-10 1.523023e-07 6.277768e-08
## GO:0090132 378/18888 3.989761e-10 1.523023e-07 6.277768e-08
## geneID Count
## GO:0071214 IGF1R/MTOR/MAPK8/CDKN1A/ATM/CASP8/PTEN/YAP1/CHEK1/ITGA2 10
## GO:0104004 IGF1R/MTOR/MAPK8/CDKN1A/ATM/CASP8/PTEN/YAP1/CHEK1/ITGA2 10
## GO:0071496 BCL2/IGF1R/MTOR/MAPK8/CDKN1A/FOXO3/CASP8/CHEK1/ITGA2/MAPK1 10
## GO:0001667 MET/AKT1/MTOR/MYH9/PTEN/PTK2/ETS1/STAT5A/FN1/ITGA2/ANLN 11
## GO:0010631 MET/AKT1/MTOR/MYH9/PTEN/PTK2/ETS1/STAT5A/ITGA2/ANLN 10
## GO:0090132 MET/AKT1/MTOR/MYH9/PTEN/PTK2/ETS1/STAT5A/ITGA2/ANLN 10
## ID Description GeneRatio BgRatio
## GO:0005925 GO:0005925 focal adhesion 7/32 421/19894
## GO:0030055 GO:0030055 cell-substrate junction 7/32 431/19894
## GO:0005826 GO:0005826 actomyosin contractile ring 2/32 4/19894
## GO:0005741 GO:0005741 mitochondrial outer membrane 5/32 219/19894
## GO:0031968 GO:0031968 organelle outer membrane 5/32 248/19894
## GO:0019867 GO:0019867 outer membrane 5/32 250/19894
## pvalue p.adjust qvalue
## GO:0005925 3.852358e-06 0.0003349071 0.0001750839
## GO:0030055 4.495397e-06 0.0003349071 0.0001750839
## GO:0005826 1.500952e-05 0.0007454729 0.0003897209
## GO:0005741 2.440940e-05 0.0009092502 0.0004753410
## GO:0031968 4.422395e-05 0.0011410129 0.0005965027
## GO:0019867 4.594683e-05 0.0011410129 0.0005965027
## geneID Count
## GO:0005925 KRAS/HSPA1A/MYH9/PTK2/ITGA2/MAPK1/TGM2 7
## GO:0030055 KRAS/HSPA1A/MYH9/PTK2/ITGA2/MAPK1/TGM2 7
## GO:0005826 MYH9/ANLN 2
## GO:0005741 BCL2/KRAS/MTOR/FOXO3/CASP8 5
## GO:0031968 BCL2/KRAS/MTOR/FOXO3/CASP8 5
## GO:0019867 BCL2/KRAS/MTOR/FOXO3/CASP8 5
## ID
## GO:0031625 GO:0031625
## GO:0044389 GO:0044389
## GO:0019902 GO:0019902
## GO:0019903 GO:0019903
## GO:0016538 GO:0016538
## GO:0140297 GO:0140297
## Description
## GO:0031625 ubiquitin protein ligase binding
## GO:0044389 ubiquitin-like protein ligase binding
## GO:0019902 phosphatase binding
## GO:0019903 protein phosphatase binding
## GO:0016538 cyclin-dependent protein serine/threonine kinase regulator activity
## GO:0140297 DNA-binding transcription factor binding
## GeneRatio BgRatio pvalue p.adjust qvalue
## GO:0031625 10/53 305/18522 1.319362e-08 4.128458e-06 1.809701e-06
## GO:0044389 10/53 324/18522 2.339069e-08 4.128458e-06 1.809701e-06
## GO:0019902 8/53 189/18522 6.065910e-08 7.137554e-06 3.128733e-06
## GO:0019903 7/53 142/18522 1.540591e-07 1.359572e-05 5.959654e-06
## GO:0016538 5/53 50/18522 3.038399e-07 2.145110e-05 9.403045e-06
## GO:0140297 10/53 478/18522 8.601058e-07 4.657057e-05 2.041412e-05
## geneID Count
## GO:0031625 RB1/HSPA1A/BID/CDKN1A/CASP8/PARP1/TUBA1B/CDKN1B/BCL2/SQSTM1 10
## GO:0044389 RB1/HSPA1A/BID/CDKN1A/CASP8/PARP1/TUBA1B/CDKN1B/BCL2/SQSTM1 10
## GO:0019902 MAPK8/PTK2/PIK3R1/CDKN1B/BCL2/MAPK1/MET/PXN 8
## GO:0019903 MAPK8/PTK2/PIK3R1/CDKN1B/BCL2/MET/PXN 7
## GO:0016538 CDKN1A/CCNE2/CCND1/CDKN1B/CASP3 5
## GO:0140297 RB1/VHL/ETS1/ARID1A/PARP1/STAT5A/BCL2/NCOA3/MYC/YAP1 10
## ID Description GeneRatio
## GO:0071214 GO:0071214 cellular response to abiotic stimulus 16/53
## GO:0104004 GO:0104004 cellular response to environmental stimulus 16/53
## GO:0051402 GO:0051402 neuron apoptotic process 14/53
## GO:0062197 GO:0062197 cellular response to chemical stress 14/53
## GO:0009411 GO:0009411 response to UV 11/53
## GO:0030099 GO:0030099 myeloid cell differentiation 15/53
## BgRatio pvalue p.adjust qvalue
## GO:0071214 334/18888 5.247375e-16 7.238754e-13 3.261658e-13
## GO:0104004 334/18888 5.247375e-16 7.238754e-13 3.261658e-13
## GO:0051402 292/18888 4.569850e-14 4.202739e-11 1.893682e-11
## GO:0062197 311/18888 1.085412e-13 7.486626e-11 3.373345e-11
## GO:0009411 154/18888 4.189669e-13 2.311859e-10 1.041684e-10
## GO:0030099 439/18888 6.861256e-13 3.155034e-10 1.421604e-10
## geneID
## GO:0071214 MTOR/MAPK8/CDKN1A/ATM/CASP8/PTEN/PARP1/IGF1R/PIK3R1/CHEK1/MYC/CASP3/YAP1/ITGA2/PIK3CA/BRCA2
## GO:0104004 MTOR/MAPK8/CDKN1A/ATM/CASP8/PTEN/PARP1/IGF1R/PIK3R1/CHEK1/MYC/CASP3/YAP1/ITGA2/PIK3CA/BRCA2
## GO:0051402 RB1/XIAP/BID/FOXO3/ATM/CASP8/KRAS/PARP1/CCND1/BCL2L11/BCL2/CASP3/PIK3CA/G6PD
## GO:0062197 HSPA1A/AKT1/MTOR/MAPK8/FOXO3/ATM/PARP1/CASP3/PIK3CA/MAPK1/G6PD/MET/PXN/PRDX1
## GO:0009411 AKT1/MAPK8/CDKN1A/PARP1/CCND1/PIK3R1/BCL2/MYC/CASP3/MSH6/BRCA2
## GO:0030099 RB1/HSPA1A/MTOR/ETS1/MYH9/FOXO3/CASP8/PARP1/PIK3R1/STAT5A/MYC/CASP3/GAB2/G6PD/FASN
## Count
## GO:0071214 16
## GO:0104004 16
## GO:0051402 14
## GO:0062197 14
## GO:0009411 11
## GO:0030099 15
## ID
## GO:0005741 GO:0005741
## GO:0031968 GO:0031968
## GO:0019867 GO:0019867
## GO:0005925 GO:0005925
## GO:0000307 GO:0000307
## GO:0061695 GO:0061695
## Description
## GO:0005741 mitochondrial outer membrane
## GO:0031968 organelle outer membrane
## GO:0019867 outer membrane
## GO:0005925 focal adhesion
## GO:0000307 cyclin-dependent protein kinase holoenzyme complex
## GO:0061695 transferase complex, transferring phosphorus-containing groups
## GeneRatio BgRatio pvalue p.adjust qvalue
## GO:0005741 7/53 219/19894 1.784906e-06 0.0002971311 0.0001654070
## GO:0031968 7/53 248/19894 4.064925e-06 0.0002971311 0.0001654070
## GO:0019867 7/53 250/19894 4.285544e-06 0.0002971311 0.0001654070
## GO:0005925 8/53 421/19894 1.449096e-05 0.0005099092 0.0002838564
## GO:0000307 4/53 56/19894 1.487873e-05 0.0005099092 0.0002838564
## GO:0061695 7/53 308/19894 1.667571e-05 0.0005099092 0.0002838564
## geneID Count
## GO:0005741 MTOR/BID/FOXO3/CASP8/KRAS/BCL2L11/BCL2 7
## GO:0031968 MTOR/BID/FOXO3/CASP8/KRAS/BCL2L11/BCL2 7
## GO:0019867 MTOR/BID/FOXO3/CASP8/KRAS/BCL2L11/BCL2 7
## GO:0005925 HSPA1A/MYH9/KRAS/PTK2/ITGA2/MAPK1/TGM2/PXN 8
## GO:0000307 RB1/CDKN1A/CCNE2/CCND1 4
## GO:0061695 RB1/CDKN1A/IGF1R/CCNE2/CCND1/PIK3R1/PIK3CA 7
## ID Description
## GO:0140297 GO:0140297 DNA-binding transcription factor binding
## GO:0106310 GO:0106310 protein serine kinase activity
## GO:0031625 GO:0031625 ubiquitin protein ligase binding
## GO:0044389 GO:0044389 ubiquitin-like protein ligase binding
## GO:0004674 GO:0004674 protein serine/threonine kinase activity
## GO:0030291 GO:0030291 protein serine/threonine kinase inhibitor activity
## GeneRatio BgRatio pvalue p.adjust qvalue
## GO:0140297 15/58 478/18522 1.296998e-11 4.046634e-09 1.870408e-09
## GO:0106310 11/58 363/18522 1.407083e-08 2.195050e-06 1.014581e-06
## GO:0031625 10/58 305/18522 3.283033e-08 3.414354e-06 1.578160e-06
## GO:0044389 10/58 324/18522 5.793200e-08 4.518696e-06 2.088601e-06
## GO:0004674 11/58 427/18522 7.387879e-08 4.610036e-06 2.130820e-06
## GO:0030291 5/58 37/18522 1.019178e-07 5.299728e-06 2.449604e-06
## geneID
## GO:0140297 RB1/VHL/ETS1/ARID1A/YWHAZ/STAT5A/NCOA3/E2F1/CDKN2A/YAP1/SMAD3/MAPK3/GATA3/CTNNB1/AR
## GO:0106310 AKT1/MTOR/MAPK8/ATM/CHEK1/MAPK9/RAF1/AKT2/PRKCA/MAPK1/MAPK3
## GO:0031625 RB1/HSPA1A/BID/CDKN1A/CASP8/YWHAZ/TUBA1B/SMAD3/CTNNB1/SQSTM1
## GO:0044389 RB1/HSPA1A/BID/CDKN1A/CASP8/YWHAZ/TUBA1B/SMAD3/CTNNB1/SQSTM1
## GO:0004674 AKT1/MTOR/MAPK8/ATM/CHEK1/MAPK9/RAF1/AKT2/PRKCA/MAPK1/MAPK3
## GO:0030291 AKT1/CDKN1A/CDKN2A/AKT1S1/RPTOR
## Count
## GO:0140297 15
## GO:0106310 11
## GO:0031625 10
## GO:0044389 10
## GO:0004674 11
## GO:0030291 5
## ID Description GeneRatio
## GO:0030099 GO:0030099 myeloid cell differentiation 19/58
## GO:0071214 GO:0071214 cellular response to abiotic stimulus 16/58
## GO:0104004 GO:0104004 cellular response to environmental stimulus 16/58
## GO:0050673 GO:0050673 epithelial cell proliferation 17/58
## GO:0051402 GO:0051402 neuron apoptotic process 14/58
## GO:0002573 GO:0002573 myeloid leukocyte differentiation 13/58
## BgRatio pvalue p.adjust qvalue
## GO:0030099 439/18888 2.547773e-17 7.625485e-14 3.320151e-14
## GO:0071214 334/18888 2.609427e-15 2.603338e-12 1.133498e-12
## GO:0104004 334/18888 2.609427e-15 2.603338e-12 1.133498e-12
## GO:0050673 482/18888 4.703462e-14 3.519365e-11 1.532338e-11
## GO:0051402 292/18888 1.799262e-13 1.077038e-10 4.689445e-11
## GO:0002573 239/18888 2.930195e-13 1.401679e-10 6.102936e-11
## geneID
## GO:0030099 RB1/HSPA1A/MTOR/ETS1/MYH9/FOXO3/CASP8/PIK3R1/STAT5A/CASP9/PRKCA/GAB2/GATA3/FASN/CTNNB1/RPTOR/G6PD/RBM15/TFRC
## GO:0071214 MTOR/MAPK8/CDKN1A/ATM/CASP8/PIK3R1/CHEK1/IGF1R/PTEN/CASP9/AKT2/YAP1/BCL2L1/MAPK3/GATA3/RPTOR
## GO:0104004 MTOR/MAPK8/CDKN1A/ATM/CASP8/PIK3R1/CHEK1/IGF1R/PTEN/CASP9/AKT2/YAP1/BCL2L1/MAPK3/GATA3/RPTOR
## GO:0050673 RB1/AKT1/BID/CDKN1A/CCND1/NRAS/STAT5A/RAF1/YAP1/BCL2L1/SMAD3/PRKCA/MAPK1/GATA3/CTNNB1/RPTOR/AR
## GO:0051402 RB1/XIAP/BID/FOXO3/ATM/CASP8/CCND1/CASP9/AKT2/BCL2L1/AKT1S1/GATA3/CTNNB1/G6PD
## GO:0002573 RB1/MTOR/MYH9/CASP8/PIK3R1/STAT5A/PRKCA/GAB2/GATA3/FASN/CTNNB1/RPTOR/TFRC
## Count
## GO:0030099 19
## GO:0071214 16
## GO:0104004 16
## GO:0050673 17
## GO:0051402 14
## GO:0002573 13
## ID Description
## GO:0031931 GO:0031931 TORC1 complex
## GO:0038201 GO:0038201 TOR complex
## GO:0031143 GO:0031143 pseudopodium
## GO:0000307 GO:0000307 cyclin-dependent protein kinase holoenzyme complex
## GO:0005925 GO:0005925 focal adhesion
## GO:0005938 GO:0005938 cell cortex
## GeneRatio BgRatio pvalue p.adjust qvalue
## GO:0031931 3/58 6/19894 4.674289e-07 0.0001177921 7.134441e-05
## GO:0038201 3/58 12/19894 5.078106e-06 0.0006398413 3.875396e-04
## GO:0031143 3/58 18/19894 1.860227e-05 0.0012155881 7.362585e-04
## GO:0000307 4/58 56/19894 2.133362e-05 0.0012155881 7.362585e-04
## GO:0005925 8/58 421/19894 2.857720e-05 0.0012155881 7.362585e-04
## GO:0005938 7/58 309/19894 3.108381e-05 0.0012155881 7.362585e-04
## geneID Count
## GO:0031931 MTOR/AKT1S1/RPTOR 3
## GO:0038201 MTOR/AKT1S1/RPTOR 3
## GO:0031143 RAF1/MAPK1/MAPK3 3
## GO:0000307 RB1/CDKN1A/CCND1/CCNE1 4
## GO:0005925 HSPA1A/MYH9/YWHAZ/MAPK1/MAPK3/CTNNB1/TGM2/PXN 8
## GO:0005938 AKT1/MYH9/AKT2/ANLN/CTNNB1/PXN/TSC1 7barplot(ego_MF[[1]], title = "enrichGO, Molecular Function, Bicluster 1 of 1")
barplot(ego_MF[[2]], title = "enrichGO, Molecular Function, Bicluster 1 of 2")
barplot(ego_MF[[3]], title = "enrichGO, Molecular Function, Bicluster 2 of 2")
barplot(ego_MF[[4]], title = "enrichGO, Molecular Function, Bicluster 1 of 3")
barplot(ego_MF[[5]], title = "enrichGO, Molecular Function, Bicluster 2 of 3")
barplot(ego_MF[[6]], title = "enrichGO, Molecular Function, Bicluster 3 of 3")
barplot(ego_MF[[7]], title = "enrichGO, Molecular Function, Bicluster 1 of 5")
barplot(ego_MF[[8]], title = "enrichGO, Molecular Function, Bicluster 2 of 5")
barplot(ego_MF[[9]], title = "enrichGO, Molecular Function, Bicluster 3 of 5")
barplot(ego_MF[[10]], title = "enrichGO, Molecular Function, Bicluster 4 of 5")
barplot(ego_MF[[11]], title = "enrichGO, Molecular Function, Bicluster 5 of 5")
barplot(ego_MF[[12]], title = "enrichGO, Molecular Function, Bicluster 1 of 10")
barplot(ego_MF[[13]], title = "enrichGO, Molecular Function, Bicluster 2 of 10")
barplot(ego_MF[[14]], title = "enrichGO, Molecular Function, Bicluster 3 of 10")
barplot(ego_MF[[15]], title = "enrichGO, Molecular Function, Bicluster 4 of 10")
#barplot(ego_MF[[16]], title = "enrichGO, Molecular Function, Bicluster 5 of 10")
barplot(ego_MF[[17]], title = "enrichGO, Molecular Function, Bicluster 6 of 10")
barplot(ego_MF[[18]], title = "enrichGO, Molecular Function, Bicluster 7 of 10")
barplot(ego_MF[[19]], title = "enrichGO, Molecular Function, Bicluster 8 of 10")
barplot(ego_MF[[20]], title = "enrichGO, Molecular Function, Bicluster 9 of 10")
barplot(ego_MF[[21]], title = "enrichGO, Molecular Function, Bicluster 10 of 10")
barplot(ego_BP[[1]], title = "enrichGO, Biological Process, Bicluster 1 of 1")
barplot(ego_BP[[2]], title = "enrichGO, Biological Process, Bicluster 1 of 2")
barplot(ego_BP[[3]], title = "enrichGO, Biological Process, Bicluster 2 of 2")
barplot(ego_BP[[4]], title = "enrichGO, Biological Process, Bicluster 1 of 3")
barplot(ego_BP[[5]], title = "enrichGO, Biological Process, Bicluster 2 of 3")
barplot(ego_BP[[6]], title = "enrichGO, Biological Process, Bicluster 3 of 3")
barplot(ego_BP[[7]], title = "enrichGO, Biological Process, Bicluster 1 of 5")
barplot(ego_BP[[8]], title = "enrichGO, Biological Process, Bicluster 2 of 5")
barplot(ego_BP[[9]], title = "enrichGO, Biological Process, Bicluster 3 of 5")
barplot(ego_BP[[10]], title = "enrichGO, Biological Process, Bicluster 4 of 5")
barplot(ego_BP[[11]], title = "enrichGO, Biological Process, Bicluster 5 of 5")
barplot(ego_BP[[12]], title = "enrichGO, Biological Process, Bicluster 1 of 10")
barplot(ego_BP[[13]], title = "enrichGO, Biological Process, Bicluster 2 of 10")
barplot(ego_BP[[14]], title = "enrichGO, Biological Process, Bicluster 3 of 10")
barplot(ego_BP[[15]], title = "enrichGO, Biological Process, Bicluster 4 of 10")
#barplot(ego_BP[[16]], title = "enrichGO, Biological Process, Bicluster 5 of 10")
barplot(ego_BP[[17]], title = "enrichGO, Biological Process, Bicluster 6 of 10")
barplot(ego_BP[[18]], title = "enrichGO, Biological Process, Bicluster 7 of 10")
barplot(ego_BP[[19]], title = "enrichGO, Biological Process, Bicluster 8 of 10")
barplot(ego_BP[[20]], title = "enrichGO, Biological Process, Bicluster 9 of 10")
barplot(ego_BP[[21]], title = "enrichGO, Biological Process, Bicluster 10 of 10")
barplot(ego_CC[[1]], title = "enrichGO, Cellular Component, Bicluster 1 of 1")
barplot(ego_CC[[2]], title = "enrichGO, Cellular Component, Bicluster 1 of 2")
barplot(ego_CC[[3]], title = "enrichGO, Cellular Component, Bicluster 2 of 2")
barplot(ego_CC[[4]], title = "enrichGO, Cellular Component, Bicluster 1 of 3")
barplot(ego_CC[[5]], title = "enrichGO, Cellular Component, Bicluster 2 of 3")
barplot(ego_CC[[6]], title = "enrichGO, Cellular Component, Bicluster 3 of 3")
barplot(ego_CC[[7]], title = "enrichGO, Cellular Component, Bicluster 1 of 5")
barplot(ego_CC[[8]], title = "enrichGO, Cellular Component, Bicluster 2 of 5")
barplot(ego_CC[[9]], title = "enrichGO, Cellular Component, Bicluster 3 of 5")
barplot(ego_CC[[10]], title = "enrichGO, Cellular Component, Bicluster 4 of 5")
barplot(ego_CC[[11]], title = "enrichGO, Cellular Component, Bicluster 5 of 5")
barplot(ego_CC[[12]], title = "enrichGO, Cellular Component, Bicluster 1 of 10")
barplot(ego_CC[[13]], title = "enrichGO, Cellular Component, Bicluster 2 of 10")
barplot(ego_CC[[14]], title = "enrichGO, Cellular Component, Bicluster 3 of 10")
barplot(ego_CC[[15]], title = "enrichGO, Cellular Component, Bicluster 4 of 10")
#barplot(ego_CC[[16]], title = "enrichGO, Cellular Component, Bicluster 5 of 10")
barplot(ego_CC[[17]], title = "enrichGO, Cellular Component, Bicluster 6 of 10")
barplot(ego_CC[[18]], title = "enrichGO, Cellular Component, Bicluster 7 of 10")
barplot(ego_CC[[19]], title = "enrichGO, Cellular Component, Bicluster 8 of 10")
barplot(ego_CC[[20]], title = "enrichGO, Cellular Component, Bicluster 9 of 10")
barplot(ego_CC[[21]], title = "enrichGO, Cellular Component, Bicluster 10 of 10")
DAG plots for ego
goplot(ego_MF[[1]]) + labs(title = "enrichGO, Molecular Function, Bicluster 1 of 1")
goplot(ego_MF[[2]]) + labs(title = "enrichGO, Molecular Function, Bicluster 1 of 2")
goplot(ego_MF[[3]]) + labs(title = "enrichGO, Molecular Function, Bicluster 2 of 2")
goplot(ego_MF[[4]]) + labs(title = "enrichGO, Molecular Function, Bicluster 1 of 3")
goplot(ego_MF[[5]]) + labs(title = "enrichGO, Molecular Function, Bicluster 2 of 3")
goplot(ego_MF[[6]]) + labs(title = "enrichGO, Molecular Function, Bicluster 3 of 3")
goplot(ego_MF[[7]]) + labs(title = "enrichGO, Molecular Function, Bicluster 1 of 5")
goplot(ego_MF[[8]]) + labs(title = "enrichGO, Molecular Function, Bicluster 2 of 5")
goplot(ego_MF[[9]]) + labs(title = "enrichGO, Molecular Function, Bicluster 3 of 5")
goplot(ego_MF[[10]]) + labs(title = "enrichGO, Molecular Function, Bicluster 4 of 5")
goplot(ego_MF[[11]]) + labs(title = "enrichGO, Molecular Function, Bicluster 5 of 5")
goplot(ego_MF[[12]]) + labs(title = "enrichGO, Molecular Function, Bicluster 1 of 10")
goplot(ego_MF[[13]]) + labs(title = "enrichGO, Molecular Function, Bicluster 2 of 10")
goplot(ego_MF[[14]]) + labs(title = "enrichGO, Molecular Function, Bicluster 3 of 10")
goplot(ego_MF[[15]]) + labs(title = "enrichGO, Molecular Function, Bicluster 4 of 10")
#goplot(ego_MF[[16]]) + labs(title = "enrichGO, Molecular Function, Bicluster 5 of 10")
goplot(ego_MF[[17]]) + labs(title = "enrichGO, Molecular Function, Bicluster 6 of 10")
goplot(ego_MF[[18]]) + labs(title = "enrichGO, Molecular Function, Bicluster 7 of 10")
goplot(ego_MF[[19]]) + labs(title = "enrichGO, Molecular Function, Bicluster 8 of 10")
goplot(ego_MF[[20]]) + labs(title = "enrichGO, Molecular Function, Bicluster 9 of 10")
goplot(ego_MF[[21]]) + labs(title = "enrichGO, Molecular Function, Bicluster 10 of 10")
goplot(ego_BP[[1]]) + labs(title = "enrichGO, Biological Process, Bicluster 1 of 1")
goplot(ego_BP[[2]]) + labs(title = "enrichGO, Biological Process, Bicluster 1 of 2")
goplot(ego_BP[[3]]) + labs(title = "enrichGO, Biological Process, Bicluster 2 of 2")
goplot(ego_BP[[4]]) + labs(title = "enrichGO, Biological Process, Bicluster 1 of 3")
goplot(ego_BP[[5]]) + labs(title = "enrichGO, Biological Process, Bicluster 2 of 3")
goplot(ego_BP[[6]]) + labs(title = "enrichGO, Biological Process, Bicluster 3 of 3")
goplot(ego_BP[[7]]) + labs(title = "enrichGO, Biological Process, Bicluster 1 of 5")
goplot(ego_BP[[8]]) + labs(title = "enrichGO, Biological Process, Bicluster 2 of 5")
goplot(ego_BP[[9]]) + labs(title = "enrichGO, Biological Process, Bicluster 3 of 5")
goplot(ego_BP[[10]]) + labs(title = "enrichGO, Biological Process, Bicluster 4 of 5")
goplot(ego_BP[[11]]) + labs(title = "enrichGO, Biological Process, Bicluster 5 of 5")
goplot(ego_BP[[12]]) + labs(title = "enrichGO, Biological Process, Bicluster 1 of 10")
goplot(ego_BP[[13]]) + labs(title = "enrichGO, Biological Process, Bicluster 2 of 10")
goplot(ego_BP[[14]]) + labs(title = "enrichGO, Biological Process, Bicluster 3 of 10")## Warning: ggrepel: 26 unlabeled data points (too many overlaps). Consider
## increasing max.overlaps
goplot(ego_BP[[15]]) + labs(title = "enrichGO, Biological Process, Bicluster 4 of 10")## Warning: ggrepel: 65 unlabeled data points (too many overlaps). Consider
## increasing max.overlaps
#goplot(ego_BP[[16]]) + labs(title = "enrichGO, Biological Process, Bicluster 5 of 10")
goplot(ego_BP[[17]]) + labs(title = "enrichGO, Biological Process, Bicluster 6 of 10")## Warning: ggrepel: 4 unlabeled data points (too many overlaps). Consider
## increasing max.overlaps
goplot(ego_BP[[18]]) + labs(title = "enrichGO, Biological Process, Bicluster 7 of 10")## Warning: ggrepel: 8 unlabeled data points (too many overlaps). Consider
## increasing max.overlaps
goplot(ego_BP[[19]]) + labs(title = "enrichGO, Biological Process, Bicluster 8 of 10")
goplot(ego_BP[[20]]) + labs(title = "enrichGO, Biological Process, Bicluster 9 of 10")
goplot(ego_BP[[21]]) + labs(title = "enrichGO, Biological Process, Bicluster 10 of 10")
goplot(ego_CC[[1]]) + labs(title = "enrichGO, Cellular Component, Bicluster 1 of 1")
goplot(ego_CC[[2]]) + labs(title = "enrichGO, Cellular Component, Bicluster 1 of 2")
goplot(ego_CC[[3]]) + labs(title = "enrichGO, Cellular Component, Bicluster 2 of 2")
goplot(ego_CC[[4]]) + labs(title = "enrichGO, Cellular Component, Bicluster 1 of 3")
goplot(ego_CC[[5]]) + labs(title = "enrichGO, Cellular Component, Bicluster 2 of 3")
goplot(ego_CC[[6]]) + labs(title = "enrichGO, Cellular Component, Bicluster 3 of 3")
goplot(ego_CC[[7]]) + labs(title = "enrichGO, Cellular Component, Bicluster 1 of 5")
goplot(ego_CC[[8]]) + labs(title = "enrichGO, Cellular Component, Bicluster 2 of 5")
goplot(ego_CC[[9]]) + labs(title = "enrichGO, Cellular Component, Bicluster 3 of 5")
goplot(ego_CC[[10]]) + labs(title = "enrichGO, Cellular Component, Bicluster 4 of 5")
goplot(ego_CC[[11]]) + labs(title = "enrichGO, Cellular Component, Bicluster 5 of 5")
goplot(ego_CC[[12]]) + labs(title = "enrichGO, Cellular Component, Bicluster 1 of 10")
goplot(ego_CC[[13]]) + labs(title = "enrichGO, Cellular Component, Bicluster 2 of 10")
goplot(ego_CC[[14]]) + labs(title = "enrichGO, Cellular Component, Bicluster 3 of 10")
goplot(ego_CC[[15]]) + labs(title = "enrichGO, Cellular Component, Bicluster 4 of 10")
#goplot(ego_CC[[16]]) + labs(title = "enrichGO, Cellular Component, Bicluster 5 of 10")
goplot(ego_CC[[17]]) + labs(title = "enrichGO, Cellular Component, Bicluster 6 of 10")
goplot(ego_CC[[18]]) + labs(title = "enrichGO, Cellular Component, Bicluster 7 of 10")
goplot(ego_CC[[19]]) + labs(title = "enrichGO, Cellular Component, Bicluster 8 of 10")
goplot(ego_CC[[20]]) + labs(title = "enrichGO, Cellular Component, Bicluster 9 of 10")
goplot(ego_CC[[21]]) + labs(title = "enrichGO, Cellular Component, Bicluster 10 of 10")
3. Export Pathway Analysis result to data
pathway = list("ggo_MF" = ggo_MF,
"ggo_BP" = ggo_BP,
"ggo_CC" = ggo_CC,
"ego_MF" = ego_MF,
"ego_BP" = ego_BP,
"ego_CC" = ego_CC)
saveRDS(pathway, file = "data/out_pathway/pathways_fabia_extracted_by_bic.rds")